I am quite happy with BWA-SW, except that it seems to generate incorrect CIGAR strings (and therefore incorrect SEQ fields) in the SAM output files. Maybe, I am confused with the output. Take a look at the two examples and please help me to understand them. I have a lot more of these, if you want more complex ones.
Example 1: reference sequence is 145 bp long, alignment starts at 92 and has 112M, meaning 92+112 > 145, right?
@SQ SN:ref1 LN:145
q1 0 ref1 92 0 65S112M148S * 0 0 CACGCACGCACGCACACACACACACACACACACACACACACACACACACACACACACACACACACGCACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACGGACACAGACACAGACAAAGACTCAGACACAAACTCAGACACAGACACAGATACAGACACAGACAAAGACACAGAAACTGAAACAGACACACAGACACAGACACAGACACAGACAAAGACACAGAAACTGAAACAGACACACAGACAC * AS:i:154 XS:i:154 XF:i:2 XE:i:0 XN:i:0
Example 2: reference sequence is 139 bp long, alignment starts at 1 and has 83M1D56M, meaning 83+1+56 > 139, right?
@SQ SN:ref2 LN:139
q2 16 ref2 1 1 92S83M1D56M201S * 0 0 GGAATTCAAAGTAATGGAAACAAACCTAGTGGAATATAATGGAATGGAAAGGACTGGAATGTAATGGAATGGATTGGAATAAACCCGATTCCAATGCAATGGAATGGAATGGAATGGAATGGAATGGAATCGAACGGAATCAACCTGAGTTTAATGGAATGGAATGGAATGGAATGAATGGAATGGAATTCAATGTAATGGAAACAAACCGAGGGGAATATAATGTAATGGAAAGGACTGGAATGTAATGGAATGGATTGGAATCAACCCGATTCCTATGCAACGGAATGGAATGTAATGGAATGGAATGGAAAGGAATGGAAAGAACTGGAATGGAATGGAATGGAATGGAATTTAATGGAATGGAATGCAATGGAATGGAATCAACCTGAGAGGAGTGGAATGGAATGGAATGGAAATGAATGGAACCGA * AS:i:73 XS:i:69 XF:i:2 XE:i:1 XN:i:0
Example 1: reference sequence is 145 bp long, alignment starts at 92 and has 112M, meaning 92+112 > 145, right?
@SQ SN:ref1 LN:145
q1 0 ref1 92 0 65S112M148S * 0 0 CACGCACGCACGCACACACACACACACACACACACACACACACACACACACACACACACACACACGCACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACGGACACAGACACAGACAAAGACTCAGACACAAACTCAGACACAGACACAGATACAGACACAGACAAAGACACAGAAACTGAAACAGACACACAGACACAGACACAGACACAGACAAAGACACAGAAACTGAAACAGACACACAGACAC * AS:i:154 XS:i:154 XF:i:2 XE:i:0 XN:i:0
Example 2: reference sequence is 139 bp long, alignment starts at 1 and has 83M1D56M, meaning 83+1+56 > 139, right?
@SQ SN:ref2 LN:139
q2 16 ref2 1 1 92S83M1D56M201S * 0 0 GGAATTCAAAGTAATGGAAACAAACCTAGTGGAATATAATGGAATGGAAAGGACTGGAATGTAATGGAATGGATTGGAATAAACCCGATTCCAATGCAATGGAATGGAATGGAATGGAATGGAATGGAATCGAACGGAATCAACCTGAGTTTAATGGAATGGAATGGAATGGAATGAATGGAATGGAATTCAATGTAATGGAAACAAACCGAGGGGAATATAATGTAATGGAAAGGACTGGAATGTAATGGAATGGATTGGAATCAACCCGATTCCTATGCAACGGAATGGAATGTAATGGAATGGAATGGAAAGGAATGGAAAGAACTGGAATGGAATGGAATGGAATGGAATTTAATGGAATGGAATGCAATGGAATGGAATCAACCTGAGAGGAGTGGAATGGAATGGAATGGAAATGAATGGAACCGA * AS:i:73 XS:i:69 XF:i:2 XE:i:1 XN:i:0
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