BWA MEM Definition of a Primary Alignment

Question

[QVINTVS_FABIVS_MAXIMVS]

Quick question:

When bwa mem splits a read into a primary and a secondary/supplementary alignment, is the primary always the "left-most" on the query or is it the more confidently mapped alignment?

Thanks.

[swbarnes2]

Secondary alignments are not the same as supplemental alignments. Secondary alignments are not split reads, they are alternate positions where the read might align.

[QVINTVS_FABIVS_MAXIMVS]

Thanks for not answering my question. For chimeric reads (i.e for this example true split-reads that for SV informative) the difference between secondary and supplementary is semantic, a secondary alignment would map to another position but be clipped in a manner that is supporting a breakpoint. Some older SV callers ask users if the -M flag was supplied in mapping.

Hence, my question: is the primary alignment considered to be the left-most on the query or the more confidently mapped alignment?

[d-cameron]

swbarnes2 answered your question regarding secondary alignments, but not supplementary alignments.

For chimeric reads (i.e for this example true split-reads that for SV informative) the difference between secondary and supplementary is semantic, a secondary alignment would map to another position but be clipped in a manner that is supporting a breakpoint.

According to the current SAM specifications, a secondary alignment is an independent alternate alignment of the entire read. A secondary alignment is a split read alignment

Old versions of the SAM specs did not have supp alignments. The -M flag is available in bwa to allow it to misreport supplementary alignments are secondary for backward compatibility with such programs.

bwa can be configured to report secondary alignments for a subset of reads using the -a, but in the general case, it does not use secondary alignments and uses it's own non-standard XA tag to write secondary alignments when the -h flag is supplied.

bwa reports alignmnet The difference between secondary and supplementary is semantic

Answer 1

[d-cameron]

The primary alignnent is not always the "left-most" on the query. This behaviour can be changed by supplying the "-5" flag in which case the alignment with the smallest coordinate will be reported as the primary.

[szp770]

Hi, it shows that bwa mem does not have -5 option.

[d-cameron]

Check you version. bwa version 0.7.17 (the latest), has the follow listed in the "Input/output options:" section:

   -5            for split alignment, take the alignment with the smallest coordinate as primary