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83 Open 334 Closed
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Issues list

Soft clip disappeared after CallMolecularConsensusReads
#1016 opened Dec 2, 2024 by jonghwanyoon
1
@tfenne
2
High number of "orphan consensus" question
#1015 opened Nov 22, 2024 by wiedenhoeft
@nh13
1
DuplexConsensusReads min-reads and max-reads-per-strand question
#1014 opened Oct 24, 2024 by saty89
@nh13
1
GroupReadsByUmi and optical duplicates question
#1013 opened Oct 14, 2024 by miwalter
1
UMI Quality enhancement help wanted question
#1008 opened Aug 22, 2024 by prot-devin
@cehtolonen
6
Snapshot releases are broken
#1005 opened Jul 31, 2024 by nh13
How to specify read structure with variable UMI length? question
#998 opened Jul 9, 2024 by bounlu
{readname} did not have a primary R1 record. (GroupReadsByUmi) help wanted question
#995 opened Jun 14, 2024 by xiechangxiao
4
feature request: add option to FilterBam to write filtered reads to separate file enhancement help wanted
#971 opened Mar 1, 2024 by eboyden
GroupReadsByUmi duplicate marking may fail when secondary and supplementary alignments are included bug
#961 opened Jan 29, 2024 by nh13
1
@tfenne
2
SetMateInformation should add the MQ tag to any supplementary alignments bug
#960 opened Jan 26, 2024 by msto
1
Support NCBI sequence_report.jsonl as input for CollectAlternateContigNames enhancement
#945 opened Oct 19, 2023 by ghuls
4
GroupReadsByUmi long runtime question
#944 opened Oct 19, 2023 by ghost
4
SamReader.query() should handle when coordinates are given < 1 or > end of contig bug
#943 opened Oct 18, 2023 by tfenne
1
@nh13
Allow multiple trim lengths or read structure in TrimFastq enhancement
#927 opened Aug 14, 2023 by bkohrn
6
Does CallMolecularConsensusReads handle overlapping fragments? question
#926 opened Aug 7, 2023 by kcibul
1
Build for 2.1.0 fails, but bumping GKL fixes it
#921 opened Jul 12, 2023 by brendes
Retaining secondary and supplementary alignments question
#920 opened Jul 7, 2023 by calcasey
2
Exact UMI from read name question
#908 opened Apr 10, 2023 by xianantwist
2
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
6
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
1
CallOverlappingConsensusBases vs "consensus-call-overlapping-bases" in CallDuplexConsensusReads
#886 opened Nov 24, 2022 by gevro
1
SetMateInformation failed question
#883 opened Nov 4, 2022 by SR5590
1
ProTip! What’s not been updated in a month: updated:<2025-01-15.