bwa: get all aligment positions of a read

Question

[mschmid]

I would like to get all the alignment positions of Illumina reads on several closely related genomes (if the aligments are above a certain aligment threshold).

So I use the the "-a" flag to output all the aligments. The problem is, that those reads get flaged as secondary.

How do I distinguish between secandary hits which are split hits (So I have to use "-M" flag as well) and the aligments which are marked secondary because a read hits multiple positions on the genomes with same/similar qual.

A small sidequestion: If a read has multiple hits on different genomes with the same mapping quality, the hit which gets reported is randomly determined, right?

[GenoMax]

Not answering your question directly but you could use bbmap.sh with multiple genome references and use the option ambig=all (in addition to any other flags you need) to allow reads to multi-map to all genomes.