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lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
GNU General Public License v3.0
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bwa mem not set proper pair flag #335

Open Frank1219 opened 3 years ago

Frank1219 commented 3 years ago

BWA-MEM command not set proper pair flag，perhaps because BWA not infer insert size characteristics. Is there some ways or tools to revise the flag value , for example revise 81 to 83, mate revise 161 to 163 ? or is there any empirical value of bwa-mem -I parameter when mapping? Thanks so much.

fredjarlier commented 2 years ago

have you try samtools fixmate?

Frank1219 commented 2 years ago

Sorry for the late reply. I had tried but it does not work. This problem can be solved by the MergeBamAlignment command of picard software, it is used for merge uBAM and BAM file. I think if there is some other parameter like it, this problem also will be solved.