I realized after I, serendipitously, ran "bwa sampe" on the same identical alignments (i.e. sai files from the same fastq) that the second mate in the pair would almost always have many mismatches. The surprising thing is that a second paired read with as many as 79 out of 101 mismatches could have a high mapping quality.
I am sure this has something to do with the Smith Waterman alignment that is attempted for the second read.
See: http://seqanswers.com/forums/showthread.php?t=14665
I have a few questions:
1) Why does bwa try and rescue reads that don't map well with bwa aln?
2) Why is the mapping quality so high when there are so many mismatches?
3) Is the reported mapping quality at the individual read level or at the pair level?
4) If I use the -s option to disable Smith-Waterman for the unmapped mate will it still use the results of the BW algorithm to get the reads in the pair that map?
I am sure this has something to do with the Smith Waterman alignment that is attempted for the second read.
See: http://seqanswers.com/forums/showthread.php?t=14665
I have a few questions:
1) Why does bwa try and rescue reads that don't map well with bwa aln?
2) Why is the mapping quality so high when there are so many mismatches?
3) Is the reported mapping quality at the individual read level or at the pair level?
4) If I use the -s option to disable Smith-Waterman for the unmapped mate will it still use the results of the BW algorithm to get the reads in the pair that map?
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