Dear all,
I used samtools mpileup in order to call the variants to compare my 12 samples. However it is hard to pick real and more confident heterozygous SNPs. I dont know how to eliminate artifact SNPs by looking vcf files.
Does anyone can help me?
Thank you so much
Aslihan
Could you help me to understand how to interprret GT:PL:GQ 0/0:0,0,0:3 what does GT 0/0 or 1/1 or 0/1
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr1 10240 . C T 4.4 . DP=4;AF1=0.6707;CI95=0.125,0.875;DP4=1,0,0,2;MQ=20;FQ=-13;PV4=0.33,0.33,1,0.032 GT:PL:GQ 0/0:0,0,0:3 0/0:0,0,0:3 0/1:20,3,0:5 0/0:0,0,0:3
0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/1:20,3,0:5 0/0:0,0,0:3 0/0:0,3,20:5 0/0:0,0,0:3
chr1 10241 . T A 4.4 . DP=4;AF1=0.6707;CI95=0.125,0.875;DP4=1,0,0,2;MQ=20;FQ=-13;PV4=0.33,1,1,0.032 GT:PL:GQ 0/0:0,0,0:3 0/0:0,0,0:3 0/1:20,3,0:5 0/0:0,0,0:3
0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/1:20,3,0:5 0/0:0,0,0:3 0/0:0,3,20:5 0/0:0,0,0:3
chr1 760912 . C T 6.26 . DP=2;AF1=1;CI95=0.2083,1;DP4=0,0,2,0;MQ=20;FQ=-25.6 GT:PL:GQ 1/1:20,3,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0
,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 1/1:18,3,0:3
chr1 822232 . T A 18.7 . DP=6;AF1=0.4727;CI95=0.04167,0.7917;DP4=2,0,3,1;MQ=20;FQ=4.94;PV4=1,0.00061,1,1 GT:PL:GQ 0/1:0,0,0:3 0/1:0,0,0:3 1/1:58,12,0:7 0/0:0,3,20:4
0/1:0,0,0:3 0/1:0,0,0:3 0/0:0,3,20:4 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3
chr1 822548 . C A 4.08 . DP=11;AF1=0.4113;CI95=0.125,0.625;DP4=0,6,0,4;MQ=20;FQ=5.58;PV4=1,1.9e-08,1,1 GT:PL:GQ 0/0:0,3,20:7 0/0:0,0,0:4 0/1:8,0,28:7 0/1:17,3,0:6
0/1:20,0,25:17 0/0:0,0,0:4 0/0:0,0,0:4 0/0:0,0,0:4 0/0:0,0,0:4 0/0:0,0,0:4 0/0:0,3,20:7 0/0:0,0,0:4
chr1 824410 . C T 32 . DP=14;AF1=0.4431;G3=2.922e-05,1,2.589e-09;HWE=0.0265;CI95=0.2083,0.625;DP4=1,7,3,3;MQ=20;FQ=34.5;PV4=0.24,0.0044,1,1 GT:PL:GQ 0/1:20,3,0:4 0/1:0
,0,0:3 0/0:0,3,20:4 0/1:0,0,0:3 0/1:8,0,45:10 0/1:0,0,0:3 0/0:0,3,20:4 0/1:0,0,0:3 0/1:14,0,14:14 0/1:9,0,14:10 0/1:31,0,11:16 0/1:0,0,0:3
chr1 825197 . G A 22.9 . DP=19;AF1=0.5279;CI95=0.25,0.75;DP4=3,2,4,1;MQ=20;FQ=26;PV4=1,7.4e-05,1,1 GT:PL:GQ 0/1:0,0,0:3 0/1:0,0,0:3 0/1:17,3,0:3 0/0:0,3,20:3
0/0:0,6,40:5 0/1:0,0,0:3 0/1:14,0,14:14 0/1:7,0,14:10 0/1:0,0,0:3 0/1:17,3,0:3 0/1:20,3,0:3 0/1:0,0,0:3
chr1 825709 . C G 30.5 . DP=11;AF1=0.494;CI95=0.2083,0.7083;DP4=5,1,4,1;MQ=20;FQ=33.5;PV4=1,8.7e-09,1,1 GT:PL:GQ 0/1:0,0,0:3 0/1:20,3,0:3 0/1:10,0,28:12 0/1:20,3,0:3
0/1:0,0,0:3 0/1:0,0,0:3 0/0:0,3,20:3 1/1:34,6,0:4 0/0:0,3,20:3 0/0:0,6,40:5 0/1:0,0,0:3 0/1:0,0,0:3
I used samtools mpileup in order to call the variants to compare my 12 samples. However it is hard to pick real and more confident heterozygous SNPs. I dont know how to eliminate artifact SNPs by looking vcf files.
Does anyone can help me?
Thank you so much
Aslihan
Could you help me to understand how to interprret GT:PL:GQ 0/0:0,0,0:3 what does GT 0/0 or 1/1 or 0/1
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr1 10240 . C T 4.4 . DP=4;AF1=0.6707;CI95=0.125,0.875;DP4=1,0,0,2;MQ=20;FQ=-13;PV4=0.33,0.33,1,0.032 GT:PL:GQ 0/0:0,0,0:3 0/0:0,0,0:3 0/1:20,3,0:5 0/0:0,0,0:3
0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/1:20,3,0:5 0/0:0,0,0:3 0/0:0,3,20:5 0/0:0,0,0:3
chr1 10241 . T A 4.4 . DP=4;AF1=0.6707;CI95=0.125,0.875;DP4=1,0,0,2;MQ=20;FQ=-13;PV4=0.33,1,1,0.032 GT:PL:GQ 0/0:0,0,0:3 0/0:0,0,0:3 0/1:20,3,0:5 0/0:0,0,0:3
0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/1:20,3,0:5 0/0:0,0,0:3 0/0:0,3,20:5 0/0:0,0,0:3
chr1 760912 . C T 6.26 . DP=2;AF1=1;CI95=0.2083,1;DP4=0,0,2,0;MQ=20;FQ=-25.6 GT:PL:GQ 1/1:20,3,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0
,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 1/1:18,3,0:3
chr1 822232 . T A 18.7 . DP=6;AF1=0.4727;CI95=0.04167,0.7917;DP4=2,0,3,1;MQ=20;FQ=4.94;PV4=1,0.00061,1,1 GT:PL:GQ 0/1:0,0,0:3 0/1:0,0,0:3 1/1:58,12,0:7 0/0:0,3,20:4
0/1:0,0,0:3 0/1:0,0,0:3 0/0:0,3,20:4 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3 0/1:0,0,0:3
chr1 822548 . C A 4.08 . DP=11;AF1=0.4113;CI95=0.125,0.625;DP4=0,6,0,4;MQ=20;FQ=5.58;PV4=1,1.9e-08,1,1 GT:PL:GQ 0/0:0,3,20:7 0/0:0,0,0:4 0/1:8,0,28:7 0/1:17,3,0:6
0/1:20,0,25:17 0/0:0,0,0:4 0/0:0,0,0:4 0/0:0,0,0:4 0/0:0,0,0:4 0/0:0,0,0:4 0/0:0,3,20:7 0/0:0,0,0:4
chr1 824410 . C T 32 . DP=14;AF1=0.4431;G3=2.922e-05,1,2.589e-09;HWE=0.0265;CI95=0.2083,0.625;DP4=1,7,3,3;MQ=20;FQ=34.5;PV4=0.24,0.0044,1,1 GT:PL:GQ 0/1:20,3,0:4 0/1:0
,0,0:3 0/0:0,3,20:4 0/1:0,0,0:3 0/1:8,0,45:10 0/1:0,0,0:3 0/0:0,3,20:4 0/1:0,0,0:3 0/1:14,0,14:14 0/1:9,0,14:10 0/1:31,0,11:16 0/1:0,0,0:3
chr1 825197 . G A 22.9 . DP=19;AF1=0.5279;CI95=0.25,0.75;DP4=3,2,4,1;MQ=20;FQ=26;PV4=1,7.4e-05,1,1 GT:PL:GQ 0/1:0,0,0:3 0/1:0,0,0:3 0/1:17,3,0:3 0/0:0,3,20:3
0/0:0,6,40:5 0/1:0,0,0:3 0/1:14,0,14:14 0/1:7,0,14:10 0/1:0,0,0:3 0/1:17,3,0:3 0/1:20,3,0:3 0/1:0,0,0:3
chr1 825709 . C G 30.5 . DP=11;AF1=0.494;CI95=0.2083,0.7083;DP4=5,1,4,1;MQ=20;FQ=33.5;PV4=1,8.7e-09,1,1 GT:PL:GQ 0/1:0,0,0:3 0/1:20,3,0:3 0/1:10,0,28:12 0/1:20,3,0:3
0/1:0,0,0:3 0/1:0,0,0:3 0/0:0,3,20:3 1/1:34,6,0:4 0/0:0,3,20:3 0/0:0,6,40:5 0/1:0,0,0:3 0/1:0,0,0:3
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