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fulcrumgenomics
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fgsv
Tools to gather evidence for structural variation via breakpoint detection.
MIT License
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#43
tfenne
closed
2 weeks ago
0
Defaulted to excluding duplicate and QC failing reads from pileup.
#42
tfenne
opened
3 months ago
2
`SvPileup` should ignore reads marked as duplicates
#41
ameynert
opened
3 months ago
3
Fix coordinate conversion for BEDPE files
#40
clintval
closed
5 months ago
1
AggregateSvPileup should report the number of reads associated with each position
#39
msto
opened
6 months ago
0
Semantic versioning is not followed on development versions
#38
nh13
opened
6 months ago
0
Add a tool to make IGV-compat. BEDPE files from AggregateSvPileup
#37
clintval
closed
6 months ago
0
Update the version of Mill and fixup all compiler warnings
#36
clintval
closed
6 months ago
0
Update SvPileup.md
#35
msto
closed
6 months ago
0
Add a description of the toolkit to the README
#34
clintval
closed
2 months ago
3
Add a DOI badge
#33
nh13
closed
9 months ago
0
Are some "Possible Deletion"s actually intra-contig rearrangements?
#32
nh13
opened
9 months ago
0
Ensure that query range used is limited to contig start/stop.
#31
tfenne
closed
1 year ago
0
Bumped toolkit and dependency versions and resolved resulting issues.
#30
tfenne
closed
1 year ago
0
Explain missing be tags in SvPileup
#29
nh13
closed
1 year ago
0
Consider circularity when finding intra-contig breakpoints
#28
jdidion
closed
1 year ago
2
Fix to AggregateSvPileup's documentation of the --bam parameter.
#27
tfenne
closed
1 year ago
0
SvPileup should allow some minimal filtering
#26
tfenne
opened
1 year ago
1
fgsv should enable easier review in IGV
#25
tfenne
opened
1 year ago
1
SvPileup should handle circular contigs better
#24
tfenne
closed
1 year ago
1
feat: add left/right template counts when aggregating pileups.
#23
nh13
closed
1 year ago
0
feat: propagate left/right target overlap annotations from SvPileup to
#22
nh13
closed
1 year ago
0
Fix typo in SvPileulp scaladocs
#21
nh13
closed
1 year ago
0
Add option BED file to SvPileup
#20
nh13
closed
1 year ago
0
bumping to 0.0.2
#19
nh13
closed
2 years ago
0
Fix Stack overflow for large clusters
#18
nh13
closed
2 years ago
0
Fix AggregateSvPileup on reads where only one end maps
#17
nh13
closed
2 years ago
0
Cannot get mate end position on read without a mapped mate.
#16
nh13
closed
2 years ago
1
SvPileup writes a query-grouped BAM, but AggregateSvPileup requires a coordinate sorted and index BAM
#15
nh13
closed
1 year ago
1
Generate docs files
#14
pamelarussell
closed
2 years ago
0
`AggregateSvPileup` should account for inaccurate split-read breakpoint positions
#13
pamelarussell
opened
2 years ago
1
Tools doc symlink broken
#12
nh13
opened
2 years ago
0
Document running the tools and any bwa mem options
#11
nh13
opened
2 years ago
0
AggregateSvPileup initial implementation
#10
pamelarussell
closed
2 years ago
1
Progress logger can count templates with no primary alignment
#9
pamelarussell
closed
2 years ago
1
SvPileup better identifies reads with SV evidence
#8
nh13
closed
2 years ago
0
More fixups of SvPileup; transition to using Metrics class; cleanup o…
#7
tfenne
closed
2 years ago
0
Add support for auto-generating docs
#6
nh13
closed
2 years ago
2
Small PR to fix pain points running on Apple silicon.
#5
tfenne
closed
2 years ago
0
Reducing EvidenceType to [SplitRead, ReadPair], adding lots of tests, support for unpaired data
#4
tfenne
closed
2 years ago
0
Lots of cleanup of the initial bolus of code.
#3
tfenne
closed
2 years ago
0
Attempting to fix breakpoint construction from alignment blocks.
#2
tfenne
closed
2 years ago
0
Initial bolus of code
#1
nh13
closed
2 years ago
1