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Old 06-19-2010, 11:16 PM   #1
baby1885
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Unhappy 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
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Old 06-20-2010, 11:32 AM   #2
nilshomer
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Quote:
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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Old 06-20-2010, 05:47 PM   #3
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Thank you nilshomer ,I have got it.
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