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bug in CallMolecularConsensusRead?

See original GitHub issue

Hello, I encountered some issues in the CallMolecularConsensus. I think the output of this program is wrong. I used the following cml java -jar fgbio-2.0.2.jar CallMolecularConsensusReads -i test.bam -o test.consensus.bam -M 1. The reads were mapped to hs37. The example input is here test.sam.txt. It is one single family.

The consensus has a T at the 44 bp from the 5’end, although all the input reads at this position have either C or N.

Issue Analytics

State:
Created a year ago
Comments:6 (3 by maintainers)

Top GitHub Comments

1reaction

ruolincommented, Jun 8, 2022

ok. I don’t have further questions. you can close it if you want.

0reactions

nh13commented, Jun 7, 2022

For duplex data, you’ll want to use --strategy adjacency. And typically one uses CallDuplexConsensusReads after that. But you can use CallMolecularConsensusReads on the output and it should create single strand reads (see https://github.com/fulcrumgenomics/fgbio/wiki/Developer-Note:-Tracking-Reads-through-Grouping-and-Duplex-Consensus-Calling for AB and BA reads)

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