hello everbody,
I have following vcf file:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 56700
chr1 14653 . C T 27 VARQ AC1=1;AF1=0.5;DP4=7,0,6,0;DP=15;FQ=29.9;FUNC=noncoding;MED=39;MQ=23;PV4=1,0.32,1,0.21;SF=0.33;VDB=0.0044;VP=0.35 GT:PL : DP:SP:GQ 0/1:57,0,72:13:0:60
can somebody please explain the QUAL column (phred quality score) of my vcf file. in the column QUAL I have values ranging from 3 to 225 (in this case 27). I guess the higher the value the more confident the calls are. but does anyone can help me with some reasonable cut offs?
thanx
I have following vcf file:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 56700
chr1 14653 . C T 27 VARQ AC1=1;AF1=0.5;DP4=7,0,6,0;DP=15;FQ=29.9;FUNC=noncoding;MED=39;MQ=23;PV4=1,0.32,1,0.21;SF=0.33;VDB=0.0044;VP=0.35 GT:PL : DP:SP:GQ 0/1:57,0,72:13:0:60
can somebody please explain the QUAL column (phred quality score) of my vcf file. in the column QUAL I have values ranging from 3 to 225 (in this case 27). I guess the higher the value the more confident the calls are. but does anyone can help me with some reasonable cut offs?
thanx
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