bwa: RNAME of chimeric reads in sam file

Question

[VHahaut]

Hello!

I am currently aligning some sequences that contain numerous chimeric reads using bwa (paired-ends). Usually, first third of the R1 is on Chr1 and the rest on Chr18, the R2 is fully mapped to Chr18.

I was wondering how bwa was aligning those reads. If we look at the sam file produced after alignment, what will be the RNAME of the read R1 (chr1 or chr18)? And how is it decided?

Thanks in advance!

Answer 1

[Pierre Lindenbaum]

BWA should create multiple SAM records for the same Read. A first SAM record will be mapped on chr1 and will contains a 'SA:X' attribute containing the alternate alignments, the cigar string will be soft-clipped. The other reads will be the instances of the 'SA:X' tag above = the other alignements, and they will be flagged as 'supplementary alignement'.

[VHahaut]

Thanks! Indeed after looking for the duplicated read names I found them.