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  • aslihan
    Member
    • Jun 2011
    • 23
    #1

    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
    Tags: None
    • Michael.James.Clark
      Senior Member
      • Apr 2009
      • 207
      #2
      Read these:
      1000genomes.org - 1000genomes Resources and Information.
      http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
      1000genomes.org is your first and best source for all of the information you’re looking for. From general topics to more of what you would expect to find here, 1000genomes.org has it all. We hope you find what you are searching for!

      Understanding VCF format - SEQanswers
      http://seqanswers.com/forums/showthread.php?t=9345&page=2
      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc
      Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
      Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
      Projects: U87MG whole genome sequence [Website] [Paper]

        Comment

        • Idon_Sokolov
          Junior Member
          • Jan 2017
          • 2
          #3
          Help

          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 I´m having problems getting my consensus calls using samTools, I already reed all the threads related to it and tried all the pileups.I´m 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?, I´m using the latest version.

          Thank you.

            Comment

            • dpryan
              Devon Ryan
              • Jul 2011
              • 3478
              #4
              So is study.vcf.gz empty or something then?

                Comment

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