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Hetrozygous / Homozygous variant ratio humans



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  • Hetrozygous / Homozygous variant ratio humans

    Hi everyone,

    Does anyone have an idea what the het/hom variant ratio is for humans?

    Is 0.7-1 reasonable depending on population for WGS

    For example, here is what I got with my GATK pipeline:

    Sample 1 (E European)

    1- After BQSR- 1.03
    2- After HaplotypeCaller- 0.73
    3- After VQSR- 0.72

    Sample 2 (Siberian):

    1- After BQSR- 1.32
    2- After HaplotypeCaller- 1.0
    3- After VQSR - 0.99

    Just trying to gauge whether my filtering is too aggressive and that I am filtering out too many true positive SNPs.

    With regards to novel SNPs:

    Sample 1:
    1- After BQSR- 10%
    2- After VQSR- 1%

    Sample 2:

    Same as sample 1

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