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fulcrumgenomics
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fgbio
Tools for working with genomic and high throughput sequencing data.
http://fulcrumgenomics.github.io/fgbio/
MIT License
308
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67
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Make ZipperBams hanlde program name collisions
#1006
bwlang
opened
2 weeks ago
1
Snapshot releases are broken
#1005
nh13
opened
2 weeks ago
0
Fix snapshot releases
#1004
nh13
closed
2 weeks ago
0
feat: raise exception if CollectDuplexSeqMetrics run on consensus BAM
#1003
znorgaard
closed
2 weeks ago
1
feat: SequenceMetadata can have name and length looked up by key
#1002
nh13
closed
1 month ago
1
Compose a `scalafmt` configuration that applies Nils and Tim's preferred conventions
#1001
msto
opened
1 month ago
1
doc: fix duplicate "the" in sequence dictionary docstrings
#1000
nh13
closed
1 month ago
1
Create CODEOWNERS
#999
nh13
closed
1 month ago
1
How to specify read structure with variable UMI length?
#998
bounlu
opened
1 month ago
0
Update ClipBam.scala
#997
yfarjoun
closed
1 month ago
2
Update Bams.scala
#996
yfarjoun
closed
1 month ago
4
{readname} did not have a primary R1 record. (GroupReadsByUmi)
#995
xiechangxiao
opened
2 months ago
4
Validate IO in SortBam to provide nicer exceptions
#994
nh13
closed
1 month ago
1
Add TemplateCoordinate sort order to the usage of SortBam
#993
nh13
closed
2 months ago
1
Warn or raise an exception when CollectDuplexSeqMetrics is run on a consensus BAM
#992
clintval
closed
2 weeks ago
0
Improve the list of tools in the README.md
#991
nh13
closed
1 month ago
1
FilterConsensusReads results too little reads compared raw fastq OR uBAM file
#990
teryyoung
opened
2 months ago
0
feat: FastqToBam can extract UMI(s) from the comment in the read name
#989
nh13
opened
3 months ago
1
Add conda install instructions to README
#988
clintval
closed
3 months ago
1
Add conda install instructions to homepage
#987
clintval
closed
3 months ago
2
The `fgbio` conda package should not require R dependencies
#986
msto
closed
3 months ago
2
Update UpdateGffContigNames.scala (typo in docs)
#985
yfarjoun
closed
3 months ago
1
Non existent path error when using FastqToBam with links
#984
shashwatsahay
closed
3 months ago
1
doc: update description of consenus tags for duplex
#983
nh13
closed
3 months ago
1
Fix codecov not finding the secret token
#982
nh13
closed
3 months ago
0
Make `PileupBuilder.includeMapPositionsOutsideFrInsert` intuitively correct
#981
clintval
closed
3 months ago
3
bug: the logic for the PileupBuilder `includeMapPositionsOutsideFrInsert` filter is wrong
#980
jrm5100
closed
3 months ago
6
GroupReadsByUmi groups reads with or without the same end.
#979
jeanquassi
closed
3 months ago
2
ZipperBams failed. Error: processed all unmapped reads but there are mapped reads remaining to be read.
#978
teryyoung
opened
4 months ago
3
Option to keep MolecularConsensusReads in CallDuplexConsensusReads
#977
karlkashofer
closed
4 months ago
3
Add support for multi-allelic variants
#976
jdidion
closed
4 months ago
1
Too up-regulated scores after fgbio CallDuplexConsensusReads
#975
VasLem
closed
4 months ago
2
Add DownsampleVcf tool
#974
TedBrookings
opened
4 months ago
1
CallMolecularConsensus Fails
#973
jmd5596
closed
5 months ago
5
GroupReadsByUmi filtered reads number does not cover all filtered reads?
#972
milnikol
opened
5 months ago
1
feature request: add option to FilterBam to write filtered reads to separate file
#971
eboyden
opened
5 months ago
0
2 Alignment steps
#970
shashwatsahay
closed
5 months ago
1
Samples processed in different lanes
#969
shashwatsahay
closed
5 months ago
4
variant calling with paired-end sequencing
#968
emmecola
closed
6 months ago
3
heap memory error
#967
subarna-slg
closed
6 months ago
1
Fix typo in ExtractUmisFromBam.scala
#966
nh13
closed
6 months ago
1
Missing space in docs
#965
mmterpstra
closed
6 months ago
1
GroupReadsByUmi may fail when marking duplicates including secondary/supplementary reads
#964
nh13
opened
6 months ago
1
fix: mapped header records should overwrite unmapped in ZipperBams
#963
nh13
closed
6 months ago
1
fix: ensure that the GroupReadsByUmiTests for marking duplicates are
#962
nh13
closed
6 months ago
1
GroupReadsByUmi duplicate marking may fail when secondary and supplementary alignments are included
#961
nh13
opened
6 months ago
2
SetMateInformation should add the MQ tag to any supplementary alignments
#960
msto
opened
6 months ago
1
Documentation for custom SAM tags from CallDuplexConsensusReads
#959
BrettLiddell
opened
6 months ago
2
feat: add --umi-prefix to CopyUmiFromReadName
#958
msto
closed
1 month ago
1
CopyUmiFromReadName should support reverse-complemented UMIs prefixed by "r"
#957
msto
opened
7 months ago
0
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