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47 Open 376 Closed
47 Open 376 Closed
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Issues list

Return pairs in ReviewConsensusVariants question
#1035 opened Feb 28, 2025 by SPPearce
@nh13
4
How should we handle missing base qualities in the consensus caller? question
#1031 opened Feb 20, 2025 by nh13
1
@nh13
6
Why do we use of hard-clipping when calculating the mate's start and end? question
#1030 opened Feb 19, 2025 by nh13
@tfenne @clintval
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
2
UMI Quality enhancement help wanted needs sponsorship
#1008 opened Aug 22, 2024 by prot-devin
7
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 enhancement
#960 opened Jan 26, 2024 by msto
@nh13
2
Support NCBI sequence_report.jsonl as input for CollectAlternateContigNames enhancement
#945 opened Oct 19, 2023 by ghuls
5
GroupReadsByUmi "identity" may be unnecessary? enhancement help wanted
#905 opened Mar 25, 2023 by eboyden
3
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
@cehtolonen
CallDuplexConsensusReads Raw Reads Filtered Due to Not Enough Reads bug needs sponsorship
#882 opened Oct 26, 2022 by ARE4S
8
AnnotateBamWithUmis, sorted or unsorted BAMs? code example? question
#879 opened Oct 13, 2022 by sofiapuvogelvittini
@cehtolonen
3
feature request: switch order of operations for ClipBam enhancement help wanted
#878 opened Oct 9, 2022 by eboyden
4
feature request: combine AssignPrimers and TrimPrimers into a single tool question
#876 opened Oct 6, 2022 by eboyden
@nh13
7
Check that alleles in calls are a subset of the variant alleles in VcfBuilder enhancement
#840 opened May 6, 2022 by nh13
Check for UMI swapping enhancement
#837 opened Apr 29, 2022 by blackbeerd
7
CigarStats.apply could give better error if internal clipping operators found enhancement
#834 opened Apr 26, 2022 by mjhipp
Feature to have ZipperBams output to SAM format
#822 opened Apr 12, 2022 by nh13
2
API Function to check for queryname or query group sorts
#799 opened Mar 1, 2022 by nh13
[bug] ClipBam: remaining aligned read bitflag not properly set when mate is clipped to 0 and unaligned
#795 opened Feb 28, 2022 by eboyden
3
[tests] Read assingment and barcodes are never checked enhancement
#788 opened Feb 24, 2022 by sstadick
1
Could --max-records-in-ram be a top-level param? question
#784 opened Feb 21, 2022 by mjhipp
6
feature request (ClipBam; other tools?): compare bam header sequence dictionary against reference to ensure they match enhancement
#748 opened Dec 17, 2021 by eboyden
4
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