Question: Getting matrix of QDs from VCF file
2.5 years ago by
Jautis • 270
Jautis • 270 wrote:
Hi, I have a vcf file and I would like to get a site-by-individual matrix of read depths (the DP label) and a second matrix of just the GQ scores.
What is the easiest way to do this? Thanks in advance!
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT samp1 samp2 chr1 100 . C T 3106.72 SnpCluster . GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,42 0/0:3,0:3:9:0,9,132 chr1 120 . C G 3106.72 SnpCluster . GT:AD:DP:GQ:PL 0/1:3,1:4:30:30,0,123 1/1:0,1:1:3:45,3,0
Ex output for DP:
1 3 4 3
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