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Accepting discordant pairs in GroupReadsByUmi #634

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ruolin opened this issue Oct 13, 2020 · 1 comment · Fixed by #648
Closed

Accepting discordant pairs in GroupReadsByUmi #634

ruolin opened this issue Oct 13, 2020 · 1 comment · Fixed by #648

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@ruolin
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ruolin commented Oct 13, 2020

Hello,
This is a new feature request.
In the note of GroupBreadsByUmi, it says

Reads are aggressively filtered out so that only high quality reads/mappings are taken forward. Paired-end reads must have both reads mapped to the same chromosome with both reads having mapping quality >= min-mapq. (Note: the MQ tag is required on reads with mapped mates).

However, we are particularly interested in the discordant pairs as we are looking for SVs. Is it possible to add a switch to loosen this restriction?

I hope this new feature also propagate to CallMolecularConsensusReads and CallDuplexConsensusReads

@nh13
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nh13 commented Dec 19, 2020

@ruolin this is a feature we haven't relaxed, but could at some point make if we have a motivating project.

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