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I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names of those reads (because I guess that primary reads with the same name are ignored?). If the tool produces something, instead of nothing (like now), then I know for sure its the supplementary read flag that could be the problem.

I use SV detection tools. The longer the reads are that I produce (like simulating improvement in the long-read sequencing technology), far less SVs gets detected, while my hypothesis is that longer reads should be able to detect more. Then I found that the alignment files look clean (sam/bam), but with far more supplementary tags. I thought I could test this by changing the flags.

I am searching the internet, but changing read flags is not something they seem to do, only things like omitting reads with certain flags from the file. Maybe I am looking with the wrong search terms, in that case I am sorry.

I guess I need to change column 1 and 2 of the sam file (QNAME and FLAG). But I was also wondering if this is going to work at all. Maybe someone with more knowledge of alignment files could help me with this problem? suggestions how to change the sam/bam file to check if supplementary reads are ignored?

I think this, because I made on purpose a very unrealistic alignment. A 15Mb region against a 15Mb region with differences (x10 times to " simulate" 10 reads / 10x coverage). The alignment file looks quite good actually in IGV, but clicking on any read reveals that there are of course MANY supplementary reads. I also have a "normal" alignment file, where I also want to check if changing the supplementary tag could possibly help me with this tool.

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