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 ,$,,,,,,,,,...,.cc.cc,+1ccccc bbbbbb`bB_\aaOaPWaTWBBYTO
chr10 7860998 * */+C 63 63 36 25 * +C 24 1 0 0 0
By the way, SAMtools pileup commond: samtools pileup -cv -f Human.genome.all.fas sort.bam
chr10 7860998 A M 83 83 36 25 ,$,,,,,,,,,...,.cc.cc,+1ccccc bbbbbb`bB_\aaOaPWaTWBBYTO
chr10 7860998 * */+C 63 63 36 25 * +C 24 1 0 0 0
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