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  • mpileup and homozygous snps

    Hi all,

    I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

    whole command (samtools-0.1.16):
    samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

    1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
    chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

    2. output of bcftools (looks heterozygous to me):
    chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

    Can anyone tell me the reason for this behaviour?
    Thank you.
    Last edited by grievous; 06-19-2011, 10:46 AM.

  • #2
    Have you solved this problem? I also have this problem, and I'm very interested in the result.

    Originally posted by grievous View Post
    Hi all,

    I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

    whole command (samtools-0.1.16):
    samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

    1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
    chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

    2. output of bcftools (looks heterozygous to me):
    chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

    Can anyone tell me the reason for this behaviour?
    Thank you.

    Comment


    • #3
      This is surely a heterozygos SNP site from A to G

      Comment


      • #4
        2. output of bcftools (looks heterozygous to me):
        chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

        I think this is heterozygous SNP, you can see this values 0/1:99

        Comment


        • #5
          Strange. One suggestion...try

          samtools mpileup -Buf my.fa my.bam | bcftools view -vcg
          The -B turns off BAQ recalculation..I've gotten strange results when it was on, which were repaired by turning it off.

          Comment


          • #6
            You could try a different SNP calling program like freebayes or gatk.

            Comment

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