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kunalkathuria
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SVXplorer
Structural Variant Caller
MIT License
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Inverted copy paste RF check on copy location
#52
kunalkathuria
closed
6 years ago
0
reduce all relevant bp margins when 1 is reduced by cluster overlap
#51
kunalkathuria
closed
6 years ago
1
Why haploid sim covg of chr X and Y ~1.5 times more in RSVSIM?
#50
kunalkathuria
closed
4 years ago
1
Move things like "calculated coverage of chr" to logging.debug
#49
kunalkathuria
closed
6 years ago
0
Update VCF header for GROUPID etc.
#48
kunalkathuria
closed
6 years ago
0
Do not use INS:ME for cut-paste and copy-paste in VCF
#47
kunalkathuria
closed
6 years ago
0
If using primaries, break loop if cluster and variant match
#46
kunalkathuria
closed
6 years ago
1
Add verbose option
#45
kunalkathuria
closed
6 years ago
1
Find a good way to get NH_REGIONS_FILE for b37 to user
#44
kunalkathuria
closed
4 years ago
1
Absolute AS Thresh should not be a fraction
#43
kunalkathuria
closed
6 years ago
0
writeDiscordants continue conditions
#42
kunalkathuria
closed
6 years ago
0
"Split INS" logic to split INS worth putting?
#41
kunalkathuria
closed
6 years ago
0
Headers for all output files
#40
kunalkathuria
closed
6 years ago
0
Add deNovo INS
#39
kunalkathuria
closed
5 years ago
1
Add INS_C check in addSR
#38
kunalkathuria
closed
6 years ago
1
INS_C overlap condition
#37
kunalkathuria
closed
6 years ago
0
Numbering in SR
#36
kunalkathuria
closed
6 years ago
0
TD overlap condition fix
#35
kunalkathuria
closed
6 years ago
0
VCF bug
#34
aakrosh
closed
6 years ago
0
Clarify meaning of "[" etc in ALT field of BND. For INV BNDs?
#33
kunalkathuria
closed
6 years ago
0
Write supporting fragments and supporting clusters as sep fields in allVariants
#32
kunalkathuria
closed
6 years ago
0
Separate SR and PE support entries in VCF
#31
kunalkathuria
closed
6 years ago
0
Incorrect specification of BND events in the VCF file
#30
aakrosh
closed
6 years ago
0
Incorrect VCF
#29
aakrosh
closed
6 years ago
0
All files written in the workspace should be tab delimited and not space delimited
#28
aakrosh
closed
6 years ago
0
Remove redundant globals from covPUFilter.py
#27
kunalkathuria
closed
6 years ago
0
Why deletion false positives in Sims if contrad by covg?
#26
kunalkathuria
closed
6 years ago
1
Normalize PU coverage for chromosome
#25
kunalkathuria
closed
6 years ago
0
Do not use flag for bnd
#24
kunalkathuria
closed
6 years ago
1
Add logging to wd.py assertion error
#23
kunalkathuria
closed
6 years ago
0
covPUFilter using 3 chars for TD check
#22
kunalkathuria
closed
6 years ago
0
Fix BEDPE output format
#21
kunalkathuria
closed
6 years ago
0
Abort and warn user if vendor-failed reads seen
#20
kunalkathuria
closed
6 years ago
0
Assertion error in writeDiscordants.py
#19
kunalkathuria
closed
6 years ago
0
Breaks if 'HD' missing in SR file header
#18
kunalkathuria
closed
6 years ago
2
Output dir msg
#17
kunalkathuria
closed
6 years ago
2
Fix makefile
#16
kunalkathuria
closed
6 years ago
0
Script to prepare discordants.bam from target.bam for user
#15
kunalkathuria
closed
6 years ago
0
Update README
#14
kunalkathuria
closed
6 years ago
0
No need to run uniqueSuppFilter twice
#13
kunalkathuria
closed
6 years ago
0
set rev margin = bp margin
#12
kunalkathuria
closed
6 years ago
0
Support for CRAM files
#11
aakrosh
opened
6 years ago
0
Script to generate discordant and splitters files from position sorted BAM
#10
aakrosh
closed
6 years ago
2
Set LIB_INV to True
#9
kunalkathuria
closed
6 years ago
0
Automate test cases for user
#8
kunalkathuria
closed
5 years ago
1
BND events missing from VCF file
#7
kunalkathuria
closed
6 years ago
0
Format the output folder
#6
aakrosh
closed
6 years ago
0
Filenames should be consistent in the output
#5
aakrosh
closed
6 years ago
0
Do not clobber the variant map file.
#4
aakrosh
closed
6 years ago
0
verbose or debug option
#3
aakrosh
closed
6 years ago
0
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