How to calculate indels per individual?
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:
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?
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Pierre Lindenbaum
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optimistsso4co3 •
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optimistsso4co3 •
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$ 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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