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 [email protected] 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 .

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