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  • SAMtools pileup result problem ~help me

    I have used SAMtools pileup call variation from illumina data,but the coming of result puzzled me as followed.ON first line it imply ref locus is 'A',but on line 2 it is '*' and '*/+C' also puzzled me,anyone who can explian for me?
    By the way, SAMtools pileup commond: samtools pileup -cv -f Human.genome.all.fas sort.bam

    chr10 7860998 A M 83 83 36 25 ,$,,,,,,,,,...,.cc.cc,+1ccccc bbbbbb`bB_\aaOaPWaTWBBYTO
    chr10 7860998 * */+C 63 63 36 25 * +C 24 1 0 0 0

  • #2
    Originally posted by baby1885 View Post
    I have used SAMtools pileup call variation from illumina data,but the coming of result puzzled me as followed.ON first line it imply ref locus is 'A',but on line 2 it is '*' and '*/+C' also puzzled me,anyone who can explian for me?
    By the way, SAMtools pileup commond: samtools pileup -cv -f Human.genome.all.fas sort.bam

    chr10 7860998 A M 83 83 36 25 ,$,,,,,,,,,...,.cc.cc,+1ccccc bbbbbb`bB_\aaOaPWaTWBBYTO
    chr10 7860998 * */+C 63 63 36 25 * +C 24 1 0 0 0
    It is calling a heterozygous A/C SNP (the first line). There is also evidence of an insertion (second line), but their is not sufficient evidence (hence the first call in the second line is a "*"). Read the samtools website's explanation carefully (http://samtools.sourceforge.net/cns0.shtml) for more information.

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    • #3
      Thank you nilshomer ,I have got it.

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