How to get depth for SNP or indel in vcf file?
Hi all!
Is there a tool that can calculate the coverage for SNP and Indel from VCF and BAM file? I have vcf file from 1000g databse and unfortunately there is NO information about read depth (eg DP).
Thank you in advance,
Best, Agata
PS. here is the line from vcf to prove that information about DP was ignored.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00119
1 69511 rs75062661 A G 100 PASS AA=.;AC=2;AF=0.65;AFR_AF=0.33;AMR_AF=0.65;AN=2;ASN_AF=0.87;AVGPOST=0.7173;ERATE=0.0237;EUR_AF=0.7;LDAF=0.6051;RSQ=0.5669;SNPSOURCE=LOWCOV;THETA=0.0052;VT=SNP GT:DS:GL 1|1:1.8:-5,-0.64,-0.11
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