Issues
- 0
IUPAC symbol Y
#1011 opened by Liukvr - 1
The option `--min-reads` in CallDuplexConsensusReads is a pre-filter and not a post-filter
#1009 opened by clintval - 0
UMI Quality
#1008 opened by prot-devin - 1
Make ZipperBams hanlde program name collisions
#1006 opened by bwlang - 0
Warn or raise an exception when CollectDuplexSeqMetrics is run on a consensus BAM
#992 opened by clintval - 0
Snapshot releases are broken
#1005 opened by nh13 - 1
Missing space in docs
#965 opened by mmterpstra - 1
Compose a `scalafmt` configuration that applies Nils and Tim's preferred conventions
#1001 opened by msto - 0
- 4
- 0
FilterConsensusReads results too little reads compared raw fastq OR uBAM file
#990 opened by teryyoung - 2
GroupReadsByUmi duplicate marking may fail when secondary and supplementary alignments are included
#961 opened by nh13 - 2
- 1
- 6
bug: the logic for the PileupBuilder `includeMapPositionsOutsideFrInsert` filter is wrong
#980 opened by jrm5100 - 2
- 3
ZipperBams failed. Error: processed all unmapped reads but there are mapped reads remaining to be read.
#978 opened by teryyoung - 3
- 2
- 5
CallMolecularConsensus Fails
#973 opened by jmd5596 - 1
- 0
feature request: add option to FilterBam to write filtered reads to separate file
#971 opened by eboyden - 1
2 Alignment steps
#970 opened by shashwatsahay - 4
Samples processed in different lanes
#969 opened by shashwatsahay - 3
variant calling with paired-end sequencing
#968 opened by emmecola - 0
- 1
heap memory error
#967 opened by subarna-slg - 1
- 2
- 0
- 2
quality score of masked N bases set to 2
#953 opened by tobyaicher - 0
- 3
Illegal option: 'ExtractUmisFromBam'
#947 opened by Neeecolaaaa - 4
- 4
GroupReadsByUmi long runtime
#944 opened by dps2501 - 0
SamReader.query() should handle when coordinates are given < 1 or > end of contig
#943 opened by tfenne - 0
Allow Bypass of assertCanWriteFile
#942 opened by greenbagels - 2
GroupReadsByUMI sorted input
#941 opened by FerriolCalvet - 2
add --barcode to FastqToBam ?
#935 opened by bwlang - 6
- 3
- 3
- 0
Broad's Artifactory URL appears to have moved
#924 opened by brendes - 1
- 3
- 0
Build for 2.1.0 fails, but bumping GKL fixes it
#921 opened by brendes - 2
Retaining secondary and supplementary alignments
#920 opened by calcasey - 1
families vs groups
#919 opened by LeilyR - 2
java.lang.OutOfMemoryError on FilterConsensusReads
#916 opened by LeilyR - 4
adding RX tag to bam files, if no fastq available
#915 opened by LeilyR