How to calculate indels per individual?
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Entering edit mode
9 months ago

I have a multi sample VCF file from whole genome sequencing and would like to generate the following table of average variant count per individual: enter image description here

Is there a tool with which you can specify variant type, like deletion, SNP, insertion, Alu, SVA etc and count number of occurance of such variants in each individual?

vcf • 201 views
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1
Entering edit mode
9 months ago
 $ bcftools stats --samples - input.vcf.gz | grep -w PSC |  cut -f3,9
[3]sample  [9]nIndels
S1         2
S2         0
S3         0
S4         3
S5         0
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