Variant calling with duplicates

Question

[storm1907]

Hello, I would like to check how viral RNA Seq called variants look before read duplicate removal. However, when I try to filter seq files with duplicates, I only have empty output

Are variant callers supposed to work with duplicates?

Thank you!

[gb]

What are you filtering? Not sure if the question is clear for every one.

But the answer is yes, variant callers can work with duplicate reads. Some times it is the default that they remove the duplicates but the variant callers do that based on a tag in the sam/bam file. If you don't add that tag it will use all reads for sure. Maybe others can give a better answer if you tell which variant caller you are using.