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  • Samtools mpileup vcf format question

    Hello,
    I have Samtools mpileup output files in VCF format. I would like to know briefly about some of the output filelds.

    How are the field values for PL:GT:GQ and PV4 calculated and what is the inference of these fields in SNPs and INDELS finding.

    Following are the example lines from VCF file.

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_4s_5s.bam
    1 49820 . T C 54.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=60 PL:GT:GQ 87,12,0:1/1:72
    1 49826 . G C 63.5 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=2,2,3,1;MQ=60;PV4=1, 0.0015,1,1 PL:GT:GQ 66,0,102:0/1:69

    It would be really helpful if anybody would give brief explanation about how these field values are obtained.

    Ketaki

  • #2
    Originally posted by k2bhide View Post
    Hello,
    I have Samtools mpileup output files in VCF format. I would like to know briefly about some of the output filelds.

    How are the field values for PL:GT:GQ and PV4 calculated and what is the inference of these fields in SNPs and INDELS finding.

    Following are the example lines from VCF file.

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_4s_5s.bam
    1 49820 . T C 54.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=60 PL:GT:GQ 87,12,0:1/1:72
    1 49826 . G C 63.5 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=2,2,3,1;MQ=60;PV4=1, 0.0015,1,1 PL:GT:GQ 66,0,102:0/1:69

    It would be really helpful if anybody would give brief explanation about how these field values are obtained.

    Ketaki
    pls visit http://seqanswers.com/forums/showthread.php?t=9345

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