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Old 07-29-2017, 02:14 PM   #1
Junior Member
Location: United states

Join Date: Jul 2017
Posts: 2
Lightbulb 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
Ghani is offline   Reply With Quote

bqsr, vqsr

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