Count number of variants per sample

Question

[r.kalampaliki]

Hello!

I have two VCF files as output of the gatk pipeline, one for including the snps and one the indels. I would like to count the number of snps and the number of indels per sample. The VCF files correspond to 30 samples, from which I am interested in 11, that I have listed in my_samples_list.txt.

My code:

while read sample_name;
do
        n_indels=$(bcftools view -s $sample_name recal_indels.vcf | grep -v "^#" | wc -l)
        n_snps=$(bcftools view -s $sample_name recal_snps.vcf | grep -v "^#" | wc -l)
        printf "%s\t%s\t%s\n" "$sample_name" "$n_snps" "$n_indels" >> n_of_variants.txt
done < ./my_samples_list.txt

Desired output:

sample_name #_snps #_indels
HG00321 111 222
HG00323 333 444

Answer 1

[Pierre Lindenbaum]

$ bcftools stats --samples - input.vcf.gz | grep PSC

# PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels.
# PSC   [2]id   [3]sample   [4]nRefHom  [5]nNonRefHom   [6]nHets    [7]nTransitions [8]nTransversions   [9]nIndels  [10]average depth   [11]nSingletons [12]nHapRef [13]nHapAlt [14]nMissing
PSC 0   S1  36  2   5   3   4   2   0.0 9   0   0   0
PSC 0   S2  30  8   7   1   14  0   0.0 0   0   0   0
PSC 0   S3  30  8   7   1   14  0   0.0 0   0   0   0
PSC 0   S4  31  6   5   4   7   3   0.0 13  0   0   0
PSC 0   S5  37  8   0   2   6   0   0.0 8   0   0   0