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!
2 answers
remove duplcates: http://www.htslib.org/algorithms/duplicate.html ; http://www.htslib.org/doc/samtools.html samtools markdup
Hello, you need to mark or remove duplicates, see: https://gatk.broadinstitute.org/hc/en-us/articles/360037225972-MarkDuplicates-Picard-
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You could also process your data with
clumpify.shto identify and eliminate sequence duplicates before you align: A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files