diff --git a/doc/bcftools.1 b/doc/bcftools.1 index 288a24ca6..f68c0350d 100644 --- a/doc/bcftools.1 +++ b/doc/bcftools.1 @@ -2,12 +2,12 @@ .\" Title: bcftools .\" Author: [see the "AUTHORS" section] .\" Generator: DocBook XSL Stylesheets v1.76.1 -.\" Date: 2015-03-20 11:57 GMT +.\" Date: 04/22/2015 .\" Manual: \ \& .\" Source: \ \& .\" Language: English .\" -.TH "BCFTOOLS" "1" "2015\-03\-20 11:57 GMT" "\ \&" "\ \&" +.TH "BCFTOOLS" "1" "04/22/2015" "\ \&" "\ \&" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- @@ -41,7 +41,6 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&. .SS "VERSION" .sp -This manual page was last updated \fB2015\-03\-20 11:57 GMT\fR and refers to bcftools git version \fB1\&.2\-6\-ga8d7fe9+\fR\&. .SS "BCF1" .sp The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&. @@ -1065,6 +1064,11 @@ tag to take values for \&.gen file: GT,PL,GL,GP .RS 4 convert gVCF to VCF, expanding REF blocks into sites\&. Only sites with FILTER set to "PASS" or "\&." will be expanded\&. .RE +.PP +\fB\-f, \-\-fasta\-ref\fR \fIfile\fR +.RS 4 +reference sequence in fasta format\&. Must be indexed with samtools faidx +.RE .RE .sp .it 1 an-trap @@ -1175,7 +1179,7 @@ comma\-separated list of fields in the input file\&. In the current version, the .PP \fB\-f, \-\-fasta\-ref\fR \fIfile\fR .RS 4 -reference sequence in fasta format +reference sequence in fasta format\&. Must be indexed with samtools faidx .RE .PP \fB\-s, \-\-samples\fR \fILIST\fR diff --git a/doc/bcftools.txt b/doc/bcftools.txt index df1bd8a67..07843158c 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -606,6 +606,9 @@ Create consensus sequence by applying VCF variants to a reference fasta file. convert gVCF to VCF, expanding REF blocks into sites. Only sites with FILTER set to "PASS" or "." will be expanded. +*-f, --fasta-ref* 'file':: + reference sequence in fasta format. Must be indexed with samtools faidx + ==== HAPS/SAMPLE conversion: *--hapsample2vcf* 'prefix' or 'haps-file','sample-file':: convert from haps/sample format to VCF. The columns of .haps file are @@ -674,7 +677,7 @@ Create consensus sequence by applying VCF variants to a reference fasta file. are not supported yet, missing data can be indicated with "--". *-f, --fasta-ref* 'file':: - reference sequence in fasta format + reference sequence in fasta format. Must be indexed with samtools faidx *-s, --samples* 'LIST':: list of sample names. See *<>* diff --git a/test/convert.gvcf.out b/test/convert.gvcf.out index 8f20d9c5a..d2c0fc914 100644 --- a/test/convert.gvcf.out +++ b/test/convert.gvcf.out @@ -22,38 +22,36 @@ ##FILTER= ##FILTER= ##FILTER= -##reference=file:///illumina/scripts/clia/Genomes/Homo_sapiens/UCSC/hg19_rCRS/Sequence/WholeGenomeFasta/genome.fa -##contig= +##contig= ##SnvTheta=0.001 ##IndelTheta=0.0001 -##MaxDepth_chr1=114.18 -##MaxDepth_chr10=131.73 -##MaxDepth_chr11=117.27 -##MaxDepth_chr12=116.97 -##MaxDepth_chr13=102.24 -##MaxDepth_chr14=101.55 -##MaxDepth_chr15=95.22 -##MaxDepth_chr16=111.33 -##MaxDepth_chr17=112.59 -##MaxDepth_chr18=121.86 -##MaxDepth_chr19=111.12 -##MaxDepth_chr2=121.83 -##MaxDepth_chr20=111.24 -##MaxDepth_chr21=98.43 -##MaxDepth_chr22=76.23 -##MaxDepth_chr3=120.09 -##MaxDepth_chr4=124.50 -##MaxDepth_chr5=119.82 -##MaxDepth_chr6=122.22 -##MaxDepth_chr7=120.27 -##MaxDepth_chr8=120.45 -##MaxDepth_chr9=102.48 -##MaxDepth_chrM=7005.66 -##MaxDepth_chrX=61.05 -##MaxDepth_chrY=37.17 +##MaxDepth_1=114.18 +##MaxDepth_10=131.73 +##MaxDepth_11=117.27 +##MaxDepth_12=116.97 +##MaxDepth_13=102.24 +##MaxDepth_14=101.55 +##MaxDepth_15=95.22 +##MaxDepth_16=111.33 +##MaxDepth_17=112.59 +##MaxDepth_18=121.86 +##MaxDepth_19=111.12 +##MaxDepth_2=121.83 +##MaxDepth_20=111.24 +##MaxDepth_21=98.43 +##MaxDepth_22=76.23 +##MaxDepth_3=120.09 +##MaxDepth_4=124.50 +##MaxDepth_5=119.82 +##MaxDepth_6=122.22 +##MaxDepth_7=120.27 +##MaxDepth_8=120.45 +##MaxDepth_9=102.48 +##MaxDepth_M=7005.66 +##MaxDepth_X=61.05 +##MaxDepth_Y=37.17 ##FILTER= ##gvcftools_version="0.16" -##gvcftools_cmdline="/illumina/scripts/clia/workflows/IsisWorkflow/IsisWorkflow_v2.0.13/bin/set_haploid_region --ref /illumina/scripts/clia/Genomes/Homo_sapiens/UCSC/hg19_rCRS/Sequence/WholeGenomeFasta/genome.fa --region-file /illumina/scripts/clia/workflows/IsisWorkflow/IsisWorkflow_v2.0.13/bin/../data/het_mask/ncbi37/male.bed" ##FILTER= ##FORMAT= ##INFO= @@ -74,323 +72,337 @@ ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE99 -chr22 1 . N . 0 LowGQX END=16050039;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:0 -chr22 16050040 . C . 0 LowGQX END=16050050;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:5:2:0 -chr22 16050051 . C . 0 LowGQX END=16050056;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:10:4:0 -chr22 16050057 . C . 0 LowGQX END=16050072;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:15:6:0 -chr22 16050073 . G . 0 LowGQX END=16050080;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:21:8:0 -chr22 16050081 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 -chr22 16050082 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 -chr22 16050083 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 -chr22 16050084 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 -chr22 16050085 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 -chr22 16050086 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050087 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050088 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050089 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050090 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050091 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050092 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050093 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050094 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050095 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050096 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050097 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050098 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050099 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050100 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050101 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050102 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050103 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050104 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050105 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050106 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050107 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050108 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050109 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050110 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050111 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050112 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050113 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050114 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050115 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050116 . G C 23 LowGQX SNVSB=0;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:56:23:22:0:16,6 -chr22 16050117 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050118 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050119 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050120 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050121 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050122 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050123 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050124 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050125 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050126 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050127 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050128 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050129 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050130 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050131 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050132 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050133 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050134 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050135 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050136 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050137 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050138 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050139 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050140 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050141 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050142 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050143 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050144 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050145 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050146 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050147 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050148 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050149 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050150 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050151 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050152 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050153 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050154 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050155 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050156 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050157 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050158 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050159 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050160 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050161 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050162 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050163 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050164 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050165 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050166 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050167 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050168 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050169 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050170 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050171 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050172 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050173 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050174 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050175 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050176 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050177 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050178 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050179 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050180 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050181 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050182 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050183 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050184 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050185 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050186 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050187 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050188 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050189 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050190 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050191 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050192 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050193 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050194 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050195 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050196 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050197 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050198 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050199 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050200 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050201 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050202 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050203 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050204 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050205 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050206 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050207 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050208 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050209 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050210 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050211 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050212 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050213 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050214 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050215 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050216 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:93:32:2 -chr22 16050217 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:93:32:2 -chr22 16050218 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050219 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050220 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050221 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050222 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050223 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050224 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050225 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050226 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050227 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050228 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050229 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050230 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050231 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050232 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050233 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050234 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050235 . T . 0 PASS . GT:GQX:DP:DPF 0/0:72:36:0 -chr22 16050236 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050237 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050238 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050239 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050240 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050241 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050242 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050243 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050244 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050245 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050246 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050247 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050248 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050249 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050250 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050251 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050252 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050253 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050254 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050255 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050256 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050257 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050258 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050259 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050260 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050261 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050262 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050263 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050264 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050265 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050266 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050267 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050268 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050269 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050270 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050271 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050272 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050273 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050274 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050275 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050276 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050277 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050278 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050279 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050280 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050281 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050282 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050283 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050284 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050285 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050286 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050287 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050288 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050289 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050290 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050291 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050292 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050293 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050294 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050295 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050296 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050297 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050298 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050299 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050300 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050301 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050302 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050303 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050304 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050305 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050306 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050307 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050308 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050309 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050310 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050311 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050312 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050313 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050314 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050315 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050316 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050317 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050318 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050319 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050320 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050321 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050322 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050323 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050324 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050325 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050326 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050327 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050328 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050329 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050330 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050331 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050332 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050333 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050334 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050335 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050336 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050337 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050338 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050339 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050340 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050341 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050342 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050343 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050344 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050345 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:220:74:0 -chr22 16050346 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:220:74:0 -chr22 16050347 . T . 0 HighDepth END=16050372;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:229:77:0 -chr22 16050373 . T . 0 HighDepth END=16050407;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:241:81:0 -chr22 16050408 . T . 0 HighDepth END=16050414;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:200:75:0 -chr22 16050415 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 -chr22 16050416 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 -chr22 16050417 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 -chr22 16050418 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 -chr22 16050419 . C . 0 HighDepth END=16050420;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:223:75:0 -chr22 16050421 . T . 0 PASS . GT:GQX:DP:DPF 0/0:223:75:1 -chr22 16050422 . T . 0 HighDepth END=16050427;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:223:75:0 -chr22 16050428 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050429 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050430 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050431 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050432 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050433 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050434 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050435 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050436 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050437 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050438 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050439 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050440 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050441 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050442 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050443 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050444 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050445 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050446 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050447 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050448 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050449 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050450 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050451 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050452 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050453 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050454 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050455 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050456 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050457 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050458 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050459 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050460 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050461 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050462 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050463 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050464 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050465 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 -chr22 16050466 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 1 . N . 0 LowGQX END=9;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:0 +22 10 . C . 0 LowGQX END=20;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:5:2:0 +22 21 . C . 0 LowGQX END=26;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:10:4:0 +22 27 . C . 0 LowGQX END=42;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:15:6:0 +22 43 . G . 0 LowGQX END=50;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:21:8:0 +22 51 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 +22 52 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 +22 53 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 +22 54 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 +22 55 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 +22 56 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 57 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 58 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 59 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 60 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 61 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 62 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 63 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 64 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 65 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 66 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 67 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 68 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 69 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 70 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 71 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 72 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 73 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 74 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 75 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 76 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 77 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 78 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 79 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 80 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 81 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 82 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 83 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 84 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 85 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 86 . G C 23 LowGQX SNVSB=0;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:56:23:22:0:16,6 +22 87 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 88 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 89 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 90 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 91 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 92 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 93 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 94 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 95 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 96 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 97 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 98 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 99 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 100 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 101 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 102 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 103 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 104 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 105 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 106 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 107 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 108 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 109 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 110 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 111 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 112 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 113 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 114 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 115 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 116 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 117 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 118 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 119 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 120 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 121 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 122 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 123 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 124 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 125 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 126 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 127 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 128 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 129 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 130 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 131 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 132 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 133 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 134 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 135 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 136 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 137 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 138 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 139 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 140 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 141 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 142 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 143 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 144 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 145 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 146 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 147 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 148 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 149 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 150 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 151 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 152 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 153 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 154 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 155 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 156 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 157 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 158 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 159 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 160 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 161 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 162 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 163 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 164 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 165 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 166 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 167 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 168 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 169 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 170 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 171 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 172 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 173 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 174 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 175 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 176 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 177 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 178 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 179 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 180 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 181 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 182 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 183 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 184 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 185 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 186 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:93:32:2 +22 187 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:93:32:2 +22 188 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 189 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 190 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 191 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 192 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 193 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 194 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 195 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 196 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 197 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 198 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 199 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 200 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 201 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 202 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 203 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 204 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 205 . T . 0 PASS . GT:GQX:DP:DPF 0/0:72:36:0 +22 206 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 207 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 208 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 209 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 210 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 211 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 212 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 213 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 214 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 215 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 216 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 217 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 218 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 219 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 220 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 221 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 222 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 223 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 224 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 225 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 226 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 227 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 228 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 229 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 230 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 231 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 232 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 233 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 234 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 235 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 236 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 237 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 238 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 239 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 240 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 241 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 242 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 243 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 244 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 245 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 246 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 247 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 248 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 249 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 250 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 251 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 252 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 253 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 254 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 255 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 256 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 257 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 258 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 259 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 260 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 261 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 262 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 263 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 264 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 265 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 266 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 267 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 268 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 269 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 270 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 271 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 272 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 273 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 274 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 275 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 276 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 277 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 278 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 279 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 280 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 281 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 282 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 283 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 284 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 285 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 286 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 287 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 288 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 289 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 290 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 291 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 292 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 293 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 294 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 295 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 296 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 297 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 298 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 299 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 300 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 301 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 302 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 303 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 304 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 305 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 306 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 307 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 308 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 309 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 310 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 311 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 312 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 313 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 314 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 315 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:220:74:0 +22 316 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:220:74:0 +22 317 . T . 0 HighDepth END=342;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:229:77:0 +22 343 . T . 0 HighDepth END=377;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:241:81:0 +22 378 . T . 0 HighDepth END=384;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:200:75:0 +22 385 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 +22 386 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 +22 387 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 +22 388 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 +22 389 . C . 0 HighDepth END=390;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:223:75:0 +22 391 . T . 0 PASS . GT:GQX:DP:DPF 0/0:223:75:1 +22 392 . T . 0 HighDepth END=397;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:223:75:0 +22 398 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 399 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 400 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 401 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 402 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 403 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 404 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 405 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 406 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 407 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 408 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 409 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 410 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 411 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 412 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 413 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 414 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 415 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 416 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 417 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 418 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 419 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 420 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 421 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 422 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 423 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 424 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 425 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 426 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 427 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 428 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 429 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 430 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 431 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 432 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 433 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 434 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 435 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 436 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 437 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 438 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 439 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 440 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 441 . C . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 442 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 443 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 444 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 445 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 446 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 447 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 448 . T . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 449 . A . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 450 . G . 0 PASS BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 diff --git a/test/convert.gvcf.vcf b/test/convert.gvcf.vcf index 402d57fdb..6dfc44d63 100644 --- a/test/convert.gvcf.vcf +++ b/test/convert.gvcf.vcf @@ -22,38 +22,36 @@ ##FILTER= ##FILTER= ##FILTER= -##reference=file:///illumina/scripts/clia/Genomes/Homo_sapiens/UCSC/hg19_rCRS/Sequence/WholeGenomeFasta/genome.fa -##contig= +##contig= ##SnvTheta=0.001 ##IndelTheta=0.0001 -##MaxDepth_chr1=114.18 -##MaxDepth_chr10=131.73 -##MaxDepth_chr11=117.27 -##MaxDepth_chr12=116.97 -##MaxDepth_chr13=102.24 -##MaxDepth_chr14=101.55 -##MaxDepth_chr15=95.22 -##MaxDepth_chr16=111.33 -##MaxDepth_chr17=112.59 -##MaxDepth_chr18=121.86 -##MaxDepth_chr19=111.12 -##MaxDepth_chr2=121.83 -##MaxDepth_chr20=111.24 -##MaxDepth_chr21=98.43 -##MaxDepth_chr22=76.23 -##MaxDepth_chr3=120.09 -##MaxDepth_chr4=124.50 -##MaxDepth_chr5=119.82 -##MaxDepth_chr6=122.22 -##MaxDepth_chr7=120.27 -##MaxDepth_chr8=120.45 -##MaxDepth_chr9=102.48 -##MaxDepth_chrM=7005.66 -##MaxDepth_chrX=61.05 -##MaxDepth_chrY=37.17 +##MaxDepth_1=114.18 +##MaxDepth_10=131.73 +##MaxDepth_11=117.27 +##MaxDepth_12=116.97 +##MaxDepth_13=102.24 +##MaxDepth_14=101.55 +##MaxDepth_15=95.22 +##MaxDepth_16=111.33 +##MaxDepth_17=112.59 +##MaxDepth_18=121.86 +##MaxDepth_19=111.12 +##MaxDepth_2=121.83 +##MaxDepth_20=111.24 +##MaxDepth_21=98.43 +##MaxDepth_22=76.23 +##MaxDepth_3=120.09 +##MaxDepth_4=124.50 +##MaxDepth_5=119.82 +##MaxDepth_6=122.22 +##MaxDepth_7=120.27 +##MaxDepth_8=120.45 +##MaxDepth_9=102.48 +##MaxDepth_M=7005.66 +##MaxDepth_X=61.05 +##MaxDepth_Y=37.17 ##FILTER= ##gvcftools_version="0.16" -##gvcftools_cmdline="/illumina/scripts/clia/workflows/IsisWorkflow/IsisWorkflow_v2.0.13/bin/set_haploid_region --ref /illumina/scripts/clia/Genomes/Homo_sapiens/UCSC/hg19_rCRS/Sequence/WholeGenomeFasta/genome.fa --region-file /illumina/scripts/clia/workflows/IsisWorkflow/IsisWorkflow_v2.0.13/bin/../data/het_mask/ncbi37/male.bed" ##FILTER= ##FORMAT= ##INFO= @@ -74,34 +72,34 @@ ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE99 -chr22 1 . N . 0 LowGQX END=16050039;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:0 -chr22 16050040 . C . 0 LowGQX END=16050050;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:5:2:0 -chr22 16050051 . C . 0 LowGQX END=16050056;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:10:4:0 -chr22 16050057 . C . 0 LowGQX END=16050072;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:15:6:0 -chr22 16050073 . G . 0 LowGQX END=16050080;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:21:8:0 -chr22 16050081 . C . 0 PASS END=16050085;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 -chr22 16050086 . G . 0 PASS END=16050102;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 -chr22 16050103 . T . 0 PASS END=16050115;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 -chr22 16050116 . G C 23 LowGQX SNVSB=0;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:56:23:22:0:16,6 -chr22 16050117 . T . 0 PASS END=16050131;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 -chr22 16050132 . A . 0 PASS END=16050170;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 -chr22 16050171 . G . 0 PASS END=16050215;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 -chr22 16050216 . T . 0 PASS END=16050217;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:93:32:2 -chr22 16050218 . T . 0 PASS END=16050234;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 -chr22 16050235 . T . 0 PASS . GT:GQX:DP:DPF 0/0:72:36:0 -chr22 16050236 . T . 0 PASS END=16050261;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050262 . A . 0 PASS END=16050279;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 -chr22 16050280 . G . 0 PASS END=16050287;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 -chr22 16050288 . A . 0 PASS END=16050299;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 -chr22 16050300 . G . 0 PASS END=16050309;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 -chr22 16050310 . A . 0 PASS END=16050344;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 -chr22 16050345 . C . 0 PASS END=16050346;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:220:74:0 -chr22 16050347 . T . 0 HighDepth END=16050372;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:229:77:0 -chr22 16050373 . T . 0 HighDepth END=16050407;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:241:81:0 -chr22 16050408 . T . 0 HighDepth END=16050414;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:200:75:0 -chr22 16050415 . G . 0 PASS END=16050418;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 -chr22 16050419 . C . 0 HighDepth END=16050420;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:223:75:0 -chr22 16050421 . T . 0 PASS . GT:GQX:DP:DPF 0/0:223:75:1 -chr22 16050422 . T . 0 HighDepth END=16050427;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:223:75:0 -chr22 16050428 . T . 0 PASS END=16050450;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 -chr22 16050451 . C . 0 PASS END=16050466;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 +22 1 . N . 0 LowGQX END=9;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:0 +22 10 . C . 0 LowGQX END=20;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:5:2:0 +22 21 . C . 0 LowGQX END=26;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:10:4:0 +22 27 . C . 0 LowGQX END=42;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:15:6:0 +22 43 . G . 0 LowGQX END=50;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:21:8:0 +22 51 . C . 0 PASS END=55;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:30:11:0 +22 56 . G . 0 PASS END=72;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:42:15:0 +22 73 . T . 0 PASS END=85;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:54:19:0 +22 86 . G C 23 LowGQX SNVSB=0;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:56:23:22:0:16,6 +22 87 . T . 0 PASS END=101;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:69:24:0 +22 102 . A . 0 PASS END=140;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:84:29:0 +22 141 . G . 0 PASS END=185;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:90:31:0 +22 186 . T . 0 PASS END=187;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:93:32:2 +22 188 . T . 0 PASS END=204;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:102:35:0 +22 205 . T . 0 PASS . GT:GQX:DP:DPF 0/0:72:36:0 +22 206 . T . 0 PASS END=231;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 232 . A . 0 PASS END=249;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:66:23:0 +22 250 . G . 0 PASS END=257;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:87:30:0 +22 258 . A . 0 PASS END=269;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:114:39:0 +22 270 . G . 0 PASS END=279;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:150:51:0 +22 280 . A . 0 PASS END=314;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:166:63:0 +22 315 . C . 0 PASS END=316;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:220:74:0 +22 317 . T . 0 HighDepth END=342;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:229:77:0 +22 343 . T . 0 HighDepth END=377;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:241:81:0 +22 378 . T . 0 HighDepth END=384;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:200:75:0 +22 385 . G . 0 PASS END=388;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:217:73:0 +22 389 . C . 0 HighDepth END=390;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:223:75:0 +22 391 . T . 0 PASS . GT:GQX:DP:DPF 0/0:223:75:1 +22 392 . T . 0 HighDepth END=397;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:223:75:0 +22 398 . T . 0 PASS END=420;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:178:60:0 +22 421 . C . 0 PASS END=450;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:142:54:0 diff --git a/test/gvcf.fa b/test/gvcf.fa new file mode 100644 index 000000000..45c4d5b02 --- /dev/null +++ b/test/gvcf.fa @@ -0,0 +1,9 @@ +>22 +NNNNNNNNCCTTGGCCAAGTCACTTCCTCCTTCAGGAACATTGCAGTGGGCCTAAGTGCC +TCCTCTCGGGACTGGTATGGGGACGGTCATGCAATCTGGACAACATTCACCTTTAAAAGT +TTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAG +GCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTC +CTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGC +TATCATTCATTTTCCTTGATTTGGGAGCCTAATTTCTTTAATTTAGTATGCAAGAAAACC +AATTTGGAAATATCAACTGTTTTGGAAACCTTAGACCTAGGTCATCCTTAGTAAGATCTT +CCCATTTATATAAATACTTGCAAGTAGTAGTGCCATAATT diff --git a/test/gvcf.fa.fai b/test/gvcf.fa.fai new file mode 100644 index 000000000..4f07c212e --- /dev/null +++ b/test/gvcf.fa.fai @@ -0,0 +1 @@ +22 460 4 60 61 diff --git a/test/test.pl b/test/test.pl index 24051ed82..0c8620658 100755 --- a/test/test.pl +++ b/test/test.pl @@ -174,7 +174,7 @@ test_vcf_convert($opts,in=>'convert',out=>'convert.hls.samples',args=>'-h .,.,-'); test_vcf_convert($opts,in=>'convert',out=>'convert.hs.hap',args=>'--hapsample -,.'); test_vcf_convert($opts,in=>'convert',out=>'convert.hs.sample',args=>'--hapsample .,-'); -test_vcf_convert_gvcf($opts,in=>'convert.gvcf',out=>'convert.gvcf.out',args=>'--gvcf2vcf'); +test_vcf_convert_gvcf($opts,in=>'convert.gvcf',out=>'convert.gvcf.out',fa=>'gvcf.fa',args=>'--gvcf2vcf'); test_vcf_convert_tsv2vcf($opts,in=>'convert.23andme',out=>'convert.23andme.vcf',args=>'-c ID,CHROM,POS,AA -s SAMPLE1',fai=>'23andme'); test_vcf_consensus($opts,in=>'consensus',out=>'consensus.1.out',fa=>'consensus.fa',mask=>'consensus.tab',args=>''); test_vcf_consensus_chain($opts,in=>'consensus',out=>'consensus.1.chain',chain=>'consensus.1.chain',fa=>'consensus.fa',mask=>'consensus.tab',args=>''); @@ -472,8 +472,8 @@ sub test_vcf_convert_gvcf { my ($opts,%args) = @_; bgzip_tabix_vcf($opts,$args{in}); - test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $$opts{tmp}/$args{in}.vcf.gz | grep -v ^##bcftools"); - test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} | grep -v ^##bcftools"); + test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} $$opts{tmp}/$args{in}.vcf.gz | grep -v ^##bcftools"); + test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} | grep -v ^##bcftools"); } sub test_vcf_convert_tsv2vcf { diff --git a/vcfconvert.c b/vcfconvert.c index c4d520392..f4922a17c 100644 --- a/vcfconvert.c +++ b/vcfconvert.c @@ -71,6 +71,7 @@ struct _args_t static void destroy_data(args_t *args) { + if ( args->ref ) fai_destroy(args->ref); if ( args->convert) convert_destroy(args->convert); if ( args->filter ) filter_destroy(args->filter); free(args->samples); @@ -1073,8 +1074,8 @@ static int tsv_setter_aa(tsv_t *tsv, bcf1_t *rec, void *usr) static void tsv_to_vcf(args_t *args) { - if ( !args->ref_fname ) error("Missing the --ref option\n"); - if ( !args->sample_list ) error("Missing the --samples option\n"); + if ( !args->ref_fname ) error("--tsv2vcf requires the --fasta-ref option\n"); + if ( !args->sample_list ) error("--tsv2vcf requires the --samples option\n"); args->ref = fai_load(args->ref_fname); if ( !args->ref ) error("Could not load the reference %s\n", args->ref_fname); @@ -1125,7 +1126,6 @@ static void tsv_to_vcf(args_t *args) if ( hts_close(in_fh) ) error("Close failed: %s\n", args->infname); free(line.s); - fai_destroy(args->ref); bcf_hdr_destroy(args->header); hts_close(out_fh); tsv_destroy(tsv); @@ -1167,6 +1167,11 @@ static void vcf_to_vcf(args_t *args) static void gvcf_to_vcf(args_t *args) { + if ( !args->ref_fname ) error("--gvcf2vcf requires the --fasta-ref option\n"); + + args->ref = fai_load(args->ref_fname); + if ( !args->ref ) error("Could not load the fai index for reference %s\n", args->ref_fname); + open_vcf(args,NULL); htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type)); if ( !out_fh ) error("Failed to open: %s\n", args->outfname); @@ -1202,10 +1207,15 @@ static void gvcf_to_vcf(args_t *args) continue; } bcf_update_info_int32(hdr,line,"END",NULL,0); - int pos; + int pos, len; for (pos=line->pos; pospos = pos; + char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(hdr,line->rid), line->pos, line->pos, &len); + if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", bcf_hdr_id2name(hdr,line->rid), line->pos+1); + // we have already checked above that there is only one allele, + // so fine to just update alleles with the ref allele from the fasta + bcf_update_alleles_str(hdr, line, &ref[0]); bcf_write(out_fh,hdr,line); } } @@ -1243,7 +1253,8 @@ static void usage(void) fprintf(stderr, " --vcf-ids output VCF IDs in second column instead of CHROM:POS_REF_ALT\n"); fprintf(stderr, "\n"); fprintf(stderr, "gVCF conversion:\n"); - fprintf(stderr, " --gvcf2vcf \n"); + fprintf(stderr, " --gvcf2vcf expand gVCF reference blocks\n"); + fprintf(stderr, " -f, --fasta-ref reference sequence in fasta format\n"); fprintf(stderr, "\n"); fprintf(stderr, "HAP/SAMPLE conversion (output from SHAPEIT):\n"); fprintf(stderr, " --hapsample2vcf <...> |,\n");