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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
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67
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SetMateInformation should add the MQ tag to any supplementary alignments
#960
msto
opened
7 months ago
1
Documentation for custom SAM tags from CallDuplexConsensusReads
#959
BrettLiddell
opened
7 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
PileupBuilder should not report insertions when checking the final mapped base before soft-clipping
#956
jrm5100
closed
7 months ago
1
Add a Zenodo DOI to the README
#955
nh13
closed
8 months ago
1
Allow the PairedAssigner to use UMI pairs where one is absent
#954
clintval
closed
8 months ago
8
quality score of masked N bases set to 2
#953
tobyaicher
closed
8 months ago
2
ZipperBams to produce mate score ("ms") for samtools markdup
#952
nh13
closed
7 months ago
1
ZipperBams should output the `ms` tag for `samtools markdup`
#951
nh13
closed
7 months ago
0
Addition of threading in GroupReadsByUmi and some other performance optimizations.
#950
tfenne
closed
9 months ago
1
Extend Read Structures operators for reverse-complemented structures
#949
galaxy001
opened
10 months ago
0
Restore consensus calling for pairs with only one mapped read.
#948
tfenne
closed
10 months ago
1
Illegal option: 'ExtractUmisFromBam'
#947
Neeecolaaaa
closed
10 months ago
3
Fix reference to transient MI tag in DuplexConsensusCaller
#946
clintval
closed
10 months ago
2
Support NCBI sequence_report.jsonl as input for CollectAlternateContigNames
#945
ghuls
opened
10 months ago
4
GroupReadsByUmi long runtime
#944
ghost
opened
10 months ago
4
SamReader.query() should handle when coordinates are given < 1 or > end of contig
#943
tfenne
opened
10 months ago
0
Allow Bypass of assertCanWriteFile
#942
greenbagels
opened
11 months ago
0
GroupReadsByUMI sorted input
#941
FerriolCalvet
closed
11 months ago
2
Alternative PR to add duplicate marking to GroupReadsByUmi
#940
tfenne
closed
10 months ago
4
Suggest fqtk in DemuxFastqs
#939
nh13
closed
11 months ago
1
Fix link in DemuxFastqs.scala
#938
PeteHaitch
closed
11 months ago
3
Bug Fix - SamRecordClipper.numBasesExtendingPastMate
#937
JoeVieira
opened
11 months ago
2
adds a barcode option to FastqToBam
#936
bwlang
closed
1 year ago
4
add --barcode to FastqToBam ?
#935
bwlang
closed
1 year ago
2
Mark Duplicate Bitflag & include secondary & Supplimentary Reads
#934
JoeVieira
closed
11 months ago
3
feat: add an option to store sample base qualities in the QT for FastqToBam
#933
nh13
closed
1 year ago
1
New: added Barcode qualities keeping in FastqToBam
#932
galaxy001
closed
1 year ago
6
Add tag to store barcode quality in sam for FastqToBam
#931
galaxy001
closed
1 year ago
3
The range of the value in step fgbio FilterConsensusReads
#930
Xiangnyu
closed
1 year ago
3
bugfix: ZipperBams should consume any remaining mapped reads
#929
nh13
closed
1 year ago
1
feat: allow TrimFastq to specify a length per input FASTQ
#928
nh13
closed
1 year ago
0
Allow multiple trim lengths or read structure in TrimFastq
#927
bkohrn
opened
1 year ago
6
Does CallMolecularConsensusReads handle overlapping fragments?
#926
kcibul
opened
1 year ago
1
Update broad snapshot artifactory url in build.sbt
#925
mjhipp
closed
1 year ago
0
Broad's Artifactory URL appears to have moved
#924
brendes
closed
1 year ago
0
Fix pass-QC in output FASTQ read names
#923
nh13
closed
1 year ago
0
DemuxFastqs --omit-failing-reads opposite expected behavior.
#922
gouinK
closed
1 year ago
3
Build for 2.1.0 fails, but bumping GKL fixes it
#921
brendes
opened
1 year ago
0
Retaining secondary and supplementary alignments
#920
calcasey
opened
1 year ago
2
families vs groups
#919
LeilyR
closed
1 year ago
1
Update intel gkl to 0.8.10
#918
nh13
closed
1 year ago
1
Add optional validation of kept read ratio to CorrectUmis
#917
mjhipp
closed
1 year ago
5
java.lang.OutOfMemoryError on FilterConsensusReads
#916
LeilyR
closed
1 year ago
2
adding RX tag to bam files, if no fastq available
#915
LeilyR
closed
1 year ago
4
Fix typos in alignment
#914
nh13
closed
1 year ago
0
Fix Alignment test
#913
jacarey
closed
1 year ago
2
Fix complement of W and S iupac codes.
#912
tfenne
closed
1 year ago
1
Call consensus reads in a 2*75bp sequencing setting (fwd and reverse do not overlap)
#911
ktrien
closed
1 year ago
3
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