Hi all, I had some difficulty in interpreting the mpileup output result, hope you all can help.
I had done a multiple sample calling for two samples using mpileup and parameters that i used are -BDIuf. Here's the subset of the result that i'm obtained： ##fileformat=VCFv4.1 ##samtoolsVersion=0.1.18 (r982:295) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 chr1 219 . T C 34.8 . DP=2;VDB=0.0090;AF1=1;AC1=4;DP4=0,0,1,1;MQ=50;FQ=-28.7 GT:PL:DP:GQ 1/1:0,0,0:0:3 1/1:66,6,0:2:7 chr1 314 . G A 7.8 . DP=1;AF1=1;AC1=4;DP4=0,0,0,1;MQ=50;FQ=-27.4 GT:PL:DP:GQ 0/1:0,0,0:0:3 1/1:37,3,0:1:3 chr1 375 . T C 11.3 . DP=1;AF1=1;AC1=4;DP4=0,0,1,0;MQ=50;FQ=-27.4 GT:PL:DP:GQ 1/1:41,3,0:1:4 0/1:0,0,0:0:3 chr1 376 . C T 3.02 . DP=2;AF1=0.4999;AC1=2;DP4=1,0,1,0;MQ=50;FQ=4.36;PV4=1,1,1,1 GT:PL:DP:GQ 0/0:0,3,41:1:7 0/1:33,3,0:1:7 chr1 469 . A G 255 . DP=9;VDB=0.0226;AF1=1;AC1=4;DP4=0,0,4,5;MQ=50;FQ=-41.9 GT:PL:DP:GQ 1/1:159,15,0:5:30 1/1:132,12,0:4:27 chr1 489 . T C 111 . DP=5;VDB=0.0191;AF1=1;AC1=4;DP4=0,0,0,5;MQ=50;FQ=-35.6 GT:PL:DP:GQ 1/1:91,9,0:3:18 1/1:55,6,0:2:15 chr1 890 . T C 4.61 . DP=4;AF1=0.3772;AC1=1;DP4=2,1,0,1;MQ=50;FQ=6.18;PV4=1,0.33,1,1 GT:PL:DP:GQ 0/1:37,3,0:1:6 0/0:0,9,107:3:12 chr1 943 . C A 3.55 . DP=2;AF1=0.5;AC1=2;DP4=1,0,0,1;MQ=50;FQ=3.55;PV4=1,1,1,1 GT:PL:DP:GQ 0/0:0,0,0:0:4 0/1:31,0,31:2:28 chr1 1068 . T A 7.8 . DP=1;AF1=1;AC1=4;DP4=0,0,0,1;MQ=50;FQ=-27.4 GT:PL:DP:GQ 0/1:0,0,0:0:3 1/1:37,3,0:1:3 Here's i wondering why some of the samples have got no reads covering it, yet it still display genotype call 0/1 or 1/1 or 0/0. It should be "./." for missing data from the samtools documentation. Many thanks. Nancy
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