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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