Variation Count Based On Chromosome

Question

[win]

I have a VCF file and i want the count of variations per chromosome i.e. for each chromosome how many variations found. i am aware that the command lc - w <filename> will give the count of total lines in the VCF but how could i indicate the chromosome number such as chr1, chr2 etc...

help much appreciated.

Answer 1

[Pierre Lindenbaum]

 grep -v -E '^#'  your.vcf | cut -f 1 | sort | uniq -c

Answer 2

[Vivek]

awk '! /\#/' varaints.vcf | awk '{print $1}' | sort | uniq -c