Read depth extraction

Question

[vlip]

Hello. I wanted to extract the read depth information from my vcf file. Can anyone share their her/his experience in doing this. My vcf format is like this (see below)

Thank you very much!

[iraun]

bcftools query is an option. See examples here.

Answer 1

[Pierre Lindenbaum]

bcftools query -f '[%CHROM %POS %SAMPLE %DP\n]' in.vcf