Dear community members,

I received hundreds of CRAM files which I have to run through Manta SV calling and they fail due to "Unexpected alignment name collision" - this file contains tens (out of millions) of reads which were multi-mapped, so they have 2 entries for some reads with particular IDs.

I don't care about those tens of multi-mappers, I want to keep only one alignment out of two (the random one) - what's the cheapest way to do it? Previously for WES samples I was converting bam files to fastq, realigning and removing reads with same IDs, but now I have WGS and I certainly don't want to re-map them.

If anyone has a ready-to-use script - please, share, otherwise I'll have to do something in python/samtools view myself...

UPD: Temporary solution - I do samtools view, pipe into 5-liner in Python and then pipe back to samtools view and this is the weirdest routine I've ever done in bioinformatics