Question: Are secondary alignments used by any tool?
2
gravatar for e.benn
12 months ago by
e.benn110
e.benn110 wrote:

I am trying to work out what tools use the secondary alignment feature of the sam format. My understanding is that there will always be exactly 1 primary alignment for each read, and secondary alignments could arise because the aligner cannot decide the exact best alignment.

Does BWA / other aligners emit secondary alignments?

Which downstream tools use secondary alignments? Haplotypecaller?

alignment • 443 views
ADD COMMENTlink modified 12 months ago by h.mon27k • written 12 months ago by e.benn110
4
gravatar for h.mon
12 months ago by
h.mon27k
Brazil
h.mon27k wrote:

For RNAseq quantification, RSEM, eXpress and Salmon (when quantifying reads from BAMs) include secondary alignments in their quantification. Probably all mappers output secondary alignments, but implementation details may vary, and often there are flags to alter this behaviour. For example, bwa mem -M will mark shorter split hits as secondary instead of suplementary, or STAR --outSAMprimaryFlag AllBestScore will mark all multiple alignments with the same best score as primary.

I am not aware of other tools that use secondary alignments, but this doesn't mean they don't exist.

ADD COMMENTlink modified 12 months ago • written 12 months ago by h.mon27k
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