How is HOB calculated.

[DarrianTalamantes]

In the info field of the VCF file after bcftools mpileup and call there is a parameter called HOB "Bias in the number of HOMs number". I was wondering how this is calculated, I am asking this here because I think this parameter is specific to the bcftools program.

Here is what is in the vcf file header.
##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">

[pd3]

Uh, this is calculated here https://github.com/samtools/bcftools/blob/develop/mcall.c#L578-L584 and should have been removed long time ago. It's a naive metric based on HWE assumption and should be replaced with https://github.com/samtools/bcftools/blob/develop/plugins/fill-tags.c#L500.

[DarrianTalamantes]

Thank you for your response!

…

On Tue, Jun 16, 2020 at 7:23 AM Petr Danecek ***@***.***> wrote: Uh, this is calculated here https://github.com/samtools/bcftools/blob/develop/mcall.c#L578-L584 and should have been removed long time ago. It's a naive metric based on HWE assumption and should be replaced with https://github.com/samtools/bcftools/blob/develop/plugins/fill-tags.c#L500 . — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1239 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AN22A6V26HDNLIBKVPAKWR3RW556XANCNFSM4NZZ3M2Q> .