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Old 12-15-2009, 08:59 PM   #1
Seq1234
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Default BWA Alignment Errors

BWA Alignment problems ..

It also produced a wrong CIGAR string.


NNNNNNNNNNNNNCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAGTCTGACATCA Ref
.....GGCTCAGGCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAG.......... Query (Correct Alignment)

BWA 0.5.0 (Version)

Cigar String: 3S1M4D72M

NNNNNNNNNNNNNCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAGTCTGACATCA Ref
.........T----CAGGCCAACTTCTAGTTCCTAATTTTGCAGGGAAGCTGAGACATGAGTGTTTAAAGGGTGGAAGCCTCCCAG..... BWA alignment


The 0.5.5 version showed no alignments for the same query and target sequences.
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