Soft clip disappeared after CallMolecularConsensusReads
#1016
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@jonghwanyoon I've added a test in #1026 to show where this occurs in the consensus calling process. In particular, it happens here: A read is clipped/trimmed based on if it extends past its mate. In the case that the same end is clipped on both reads, perhaps we shouldn't clip, we'll have to think about this further. In the meantime, if you'd like to sponsor this work, feel free to reach out to us. |
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@jonghwanyoon I think I found an easy fix, will need a review from the team |
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hello
When calling Molecular consensus reads using fgbio's
CallMolecularConsensusReads, the soft clip disappears.I went through
CorrectUmis,GroupReadsByUmi,CallMolecularConsensusReads,alignmenton a bam file mapped with raw fastq, and noticed that the soft clips disappeared on important singleton reads.Given the presence of soft clips in the bam file resulting from
GroupReadsByUmi, it seems that the issue is inCallMolecularConsensusReads.I only gave
CallMolecularConsensusReadsthe java option and the--min-reads=1parameter.There doesn't seem to be any parameter associated with
CallMolecularConsensusReads(I could be wrong)This is the same in
2.1.1, when collapsing between chromosomes became possible, and in2.4.0, the current latest version.Although it is a singleton read, it is an important read that represents a clinically meaningful fusion, so I don't want the soft clips to disappear.
May I request your opinion on this issue?
Thank you!
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