bwa: get all aligment positions of a read
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?
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Not answering your question directly but you could use
bbmap.shwith multiple genome references and use the optionambig=all(in addition to any other flags you need) to allow reads to multi-map to all genomes.