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Old 07-07-2010, 01:22 AM   #3
Junior Member
Location: London

Join Date: May 2010
Posts: 3
Default Mismatch threshold for both reads in a paired-end run


One of my colleagues has found that when he aligns 80bp paired-end reads using bwa that the mismatch threshold only applies to any one of the two sequences and the other can have as many mismatches as permitted. For example, one paired read can have the default two mismatches and the other paired read had 45 mismatches. Is there an option in bwa to set the mismatch level on both paired reads because it is going to be quite unproductive to have to parse the resulting SAM file. Please give me some good news with regard to phantom parameters. Look forward to hearing from you.

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