Question: What criteria are used to determine supplementary alignment with bwa-mem (flag 2048)
gravatar for annawilliford
3.0 years ago by
United States
annawilliford0 wrote:


Supplementary alignment (chimeric reads, flag 2048) is set when a read aligns to 2 or more different genome locations. What is the minimum number of bases that must align to a different location to be considered a chimeric read?  I have reads marked as SA when >25 bases align elsewhere, but not 8, for example. Does it depend on read length? I have bwa-mem alignments with 45-bp paired-end reads and none of the reads are set as SA reads (although I know they are), while alignments using 75-bp reads (same genome) have plenty of SA reads. BWA versions :0.7.7/0.7.12

Thank you!


alignment • 1.9k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 3.0 years ago by annawilliford0

The odds are good that you'll need to go through the code to find the answer to this. The paper describing bwa mem is only a page long, so details like this will be omitted.

ADD REPLYlink written 3.0 years ago by Devon Ryan81k

you could also try tagging your post bwa and hope that lh3 replies

ADD REPLYlink written 2.9 years ago by Ying W3.8k
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