How to remove reads supporting the same fragment that other reads support

Question

[jeni]

Hi, I am trying to run a variant caller which is raising an Exception error because there are more than two reads in my bam supporting the same fragment. Is there any possibility to find those reads in my bam and remove those fragments which are aligning in the same exact positions?

I have already removed duplicates and the problem persist. I think this is more related to suplementary alignments due to some artifact in my library.

Thanks!

[GenoMax]

You could also process your data with clumpify.sh to identify and eliminate sequence duplicates before you align: A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files

Answer 1

[Pierre Lindenbaum]

remove duplcates: http://www.htslib.org/algorithms/duplicate.html ; http://www.htslib.org/doc/samtools.html samtools markdup

[jeni]

I have already removed duplicates, but I think my library has some artifact and I think this is more related to suplementary alignments

Answer 2

[MatthewP]

Hello, you need to mark or remove duplicates, see: https://gatk.broadinstitute.org/hc/en-us/articles/360037225972-MarkDuplicates-Picard-