How to calculate indels per individual?

Question

[optimistsso4co3]

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?

Answer 1

[Pierre Lindenbaum]

 $ 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