Entering edit mode
6.6 years ago
ATpoint
81k
We have some alignment lying around that were initially mapped to the human genome, in which the ref-fasta contained all the major chromosomes including the ALT contigs, but without that BWA mem was used in ALT-aware mode. This of course created some/many (I don't know exactly) matches with low or 0 MAPQ. Is there any way to post-process these files in order to account for the ALTs? As the files are large and numerous, please do not suggest to convert them back to fastq, because that is actually what I would like to avoid.
