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Old 07-22-2011, 09:33 AM   #1
aslihan
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Default Samtools-mpileup

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
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Old 07-22-2011, 10:02 AM   #2
Michael.James.Clark
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Read these:
http://www.1000genomes.org/wiki/Anal...mat-version-41
http://seqanswers.com/forums/showthr...?t=9345&page=2
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Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
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Old 01-18-2017, 03:56 PM   #3
Idon_Sokolov
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Quote:
Originally Posted by aslihan View Post
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
Hello, sorry to disturb you, but Im having problems getting my consensus calls using samTools, I already reed all the threads related to it and tried all the pileups.Im using this command:

samtools mpileup -ugf Homo_sapiens.GRCh38.dna.alt.fa.gz aln.sorted.bam | bcftools call -vmO z -o study.vcf.gz

But this is my result:
[main] Unrecognized command.
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

Could you please help me?, Im using the latest version.

Thank you.
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Old 01-18-2017, 10:53 PM   #4
dpryan
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So is study.vcf.gz empty or something then?
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