Question: how to output the best alignment rather than multiple alignments for each read in BWA
gravatar for zhangdengwei
6 weeks ago by
zhangdengwei30 wrote:

Dear all, I would like to use BWA mem to output the best alignment for each read instead of all alignments, just like the "-k" argument below in Bowtie2, however, I haven't found the same function in BWA mem, which my version is 0.7.17-r1188, did I miss something or how can I tackle it?

  -k <int>           report up to <int> alns per read; MAPQ not meaningful
  -a/--all           report all alignments; very slow, MAPQ not meaningful
alignment • 128 views
ADD COMMENTlink modified 5 weeks ago by d-cameron2.0k • written 6 weeks ago by zhangdengwei30
gravatar for d-cameron
5 weeks ago by
d-cameron2.0k wrote:

did I miss something

Reporting only the best alignment is the default in bwa mem (and bowtie2). By default, bwa reports some alternate alignments in the XA tag but you can ignore that. Note that for some reads the best alignment is chimeric so multiple alignment record will be reported for that read, linked by the SA tag. Note that these record collectively form a single alignment and are not considered to be alternate alignments.

ADD COMMENTlink written 5 weeks ago by d-cameron2.0k
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