Do I need to keep unmapped sequence on Variant calling?

Question

[khanhlpbao]

I saw some Pipeline for Variation calling and none of them included the removal of unmapped sequences through samtools or similar tools. Does I need to keep all of them or I can filtered out them? I'm going to analyze the variant from 50 SE MGI DNB sequencing. thank you very much

Answer 1

[ATpoint]

Since they're unmapped they do not contribute to standard variant calling, so one could filter them out. Still, having also the unmapped reads in the BAM files allows to convert back bam to fastq which can be convenient sometimes plus filtering is an additional step that is not necessary. You can do it, but don't have to.