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Use GroupReadsByUmi for standard duplicate marking?
enhancement
help wanted
#906
opened Mar 25, 2023 by
eboyden
GroupReadsByUmi "identity" may be unnecessary?
enhancement
help wanted
#905
opened Mar 25, 2023 by
eboyden
ZipperBams error about RGID
enhancement
help wanted
question
#902
opened Feb 6, 2023 by
esamorodnitsky
CallMolecularConsensusReads vs. CallOverlappingConsensusBases vs. CallDuplexConsensusReads
#899
opened Feb 2, 2023 by
esamorodnitsky
Write a guide on "so you have UMIs in your data, here's how to get to a standardized BAM" with fgbio
#890
opened Dec 8, 2022 by
nh13
require-single-strand-agreement on BAM that contains both duplex and single-strand consensus reads
#889
opened Nov 25, 2022 by
gevro
CallOverlappingConsensusBases vs "consensus-call-overlapping-bases" in CallDuplexConsensusReads
#886
opened Nov 24, 2022 by
gevro
CallDuplexConsensusReads Raw Reads Filtered Due to Not Enough Reads
bug
#882
opened Oct 26, 2022 by
ARE4S
SetMateInformation: Input is not queryname sorted or grouped
#880
opened Oct 17, 2022 by
sofiapuvogelvittini
AnnotateBamWithUmis, sorted or unsorted BAMs? code example?
question
#879
opened Oct 13, 2022 by
sofiapuvogelvittini
feature request: switch order of operations for ClipBam
enhancement
help wanted
#878
opened Oct 9, 2022 by
eboyden
question: need to correct MD/NM/UQ tags multiple times on piped commands or not?
#877
opened Oct 8, 2022 by
eboyden
feature request: combine AssignPrimers and TrimPrimers into a single tool
question
#876
opened Oct 6, 2022 by
eboyden
Check that alleles in calls are a subset of the variant alleles in VcfBuilder
enhancement
#840
opened May 6, 2022 by
nh13
CigarStats.apply
could give better error if internal clipping operators found
enhancement
#834
opened Apr 26, 2022 by
mjhipp
FilterConsensusReads --min-reads 1 0 0 vs --min-reads 0 0 0; Why do they differ?
question
#833
opened Apr 26, 2022 by
dennis-serum
CallDuplexConsensusReads hard-clips ONE of the two duplex reads
question
#831
opened Apr 25, 2022 by
genegolts
The minimum number of reads supporting a consensus base/read.
question
#830
opened Apr 25, 2022 by
asmlgkj
Should consensus calling trim back to the _unclipped end_ versus the aligned end of its mate
question
#828
opened Apr 21, 2022 by
nh13
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