Count number of InDels per chromosome in Raw vcf file

Question

[mostafarafiepour]

Hello to all,

I want to count the number of InDels for each chromosome in the Raw VCF file.

What is the best idea?

Best Regard

Mostafa

[Pierre Lindenbaum]

see How to count SNPs, InDels , Count Of Variants , SNP,INDEL counting per chromosomes in vcf

[mostafarafiepour]

many thanks for your reply,

Now, if i want to count the number of SNPs for each Breed, what is the best idea?

i have 5 breed in the my raw vcf.

[mostafarafiepour]

I used these two scripts to count insertions and deletions, but the output was zero?

insertions:

awk '! /\#/' variants.vcf | awk '{if(length($4) > 1 ) print}' | wc -l

deletions:

awk '! /\#/' variants.vcf | awk '{if(length($5) > 1) print}' | wc -l

[GenoMax]

That is not the solution posted in A: How to count SNPs, InDels

[ATpoint]

That is not a good solution, as you might have variants with multiple alleles, see this example:

chr1    10812   rs1197106884    G       C,T     .       .       RS=1197106884;RSPOS=10812;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99756307339449541,0.00242896279306829,0.00000796381243628

This would be a InDel count with your script, but is a SNP. Refer to the offered solutions.

Answer 1

[Alex Reynolds]

Via BEDOPS convert2bed:

$ vcf2bed --snvs < foo.vcf | wc -l
$ vcf2bed --insertions < foo.vcf | wc -l
$ vcf2bed --deletions < foo.vcf | wc -l