can you confirm this:
one of my bam was aligned with an 'old' version of BWA:
@PG ID:bwa PN:bwa VN:0.6.2-r126
some reads length=100 are said to have a cigar string 100M and an edit distance of NM:i:2
HWI-1KL149:59:C2AVTACXX:5:2209:15195:25860 147 1 12106 0 100M = 11987 -219 TGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATAT JHGEIK7KLKKJL7JFIHILGE@@?CCBBDBABC?BBCABBABAAB@AF?BB@BB?BB??BABB???BCCCBBAC?AA>BBBBBBGECADDG==6)'#%# X0:i:6 X1:i:1 BD:Z:NINNPONMMMNONNNMNNPOOOKKOPMMMMONPOONOMNLMNMLLKNNMONMNMMOONNONNLMIIMLDLLMLLNMMMMLDLLLNNMLKNMLMMLHMJKK MD:Z:98C0A0 PG:Z:MarkDuplicates.13 RG:Z:p55 XG:i:0 BI:Z:RNQRRRPPNQQRSQQRRQSSRSNNRSPRRPRQSRQSSPSPOSRPPPRRRRQQRNRRQSQQSQQRNOQPKPQQRRRRQRQPKPQQRRQRPRQQQRPQQPPP AM:i:0 NM:i:2 SM:i:0 XM:i:2 XO:i:0 MQ:i:0 XT:A:R
furthermore blat said that two bases in 3' shoudl be soft-clipped (alignment goes from 1 to 98 instead of 1 to 100):
00001 tgggccattgttcatcttctggcccctgttgtctgcatgtaacttaatac 00050
>>>>> |||||||||||||||||||||||||||||||||||||||||||||||||| >>>>>
12106 tgggccattgttcatcttctggcccctgttgtctgcatgtaacttaatac 12155
00051 cacaaccaggcataggggaaagattggaggaaagatgagtgagagcat 00098
>>>>> |||||||||||||||||||||||||||||||||||||||||||||||| >>>>>
12156 cacaaccaggcataggggaaagattggaggaaagatgagtgagagcat 12203
So I would have expected that the cigar string would have been 98M2S instead of 100M.
Can you confirm this ? Is it a 'feature' of bwa or is it fixed in the latest version of bwa ?
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written
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Pierre Lindenbaum
I would say both answers are correct. It all depends on what scoring is.
As long as the penalty for mismatch is smaller than that of clipping you'll get the first answer. Of course now we also have a mismatch towards the end of the read where allowing clipping makes more sense.
but bwa is a local alignment isn't it ? so scoring/mismatch at 5' or/and 3' makes no sense to me.
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written
by
Pierre Lindenbaum
no it is a semi-global aligner, it tries as much as it can to align the entire read.
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