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kunalkathuria
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SVXplorer
Structural Variant Caller
MIT License
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Bump scipy from 1.2.2 to 1.10.0
#102
dependabot[bot]
opened
1 year ago
0
Missing genotype GT in VCF files?
#101
pauline-ng
closed
1 year ago
1
Bump numpy from 1.16.5 to 1.22.0
#100
dependabot[bot]
opened
2 years ago
0
Fixes #97
#99
sienkie
closed
3 years ago
0
Reads passing vendor checks
#98
burnsro
closed
3 years ago
4
Unable to install SVXplorer
#97
neharajkumar
closed
3 years ago
7
Memory and ALT
#96
waschf
closed
4 years ago
4
Memory needed to run?
#95
Solyris83
closed
4 years ago
1
Fix #93
#94
kunalkathuria
closed
4 years ago
0
SVXplorer pip install errors
#93
ghost
closed
4 years ago
5
Find variant in a cohort
#92
ghost
closed
4 years ago
6
Undefined variable
#91
aakrosh
closed
4 years ago
1
Undefined variable 'argparse'
#90
aakrosh
closed
4 years ago
0
Using variable 'prevTID' before assignment
#89
aakrosh
closed
4 years ago
2
No value for argument 'maxClusterMargin' in function call in addSplitReads.py
#88
aakrosh
closed
4 years ago
1
Duplicated parts of code
#87
sienkie
closed
4 years ago
0
Pre PyPI release changes
#86
sienkie
opened
4 years ago
0
Missing parsers for command line tools
#85
sienkie
closed
4 years ago
1
Missing argument in addSplitReads.py
#84
sienkie
closed
4 years ago
0
CR tag in INFO
#83
aakrosh
closed
5 years ago
1
Distribution
#82
aakrosh
opened
5 years ago
0
Handle multiple read-groups
#81
aakrosh
opened
5 years ago
0
Ensure no duplicate fxns if contained in shared.py
#80
kunalkathuria
closed
6 years ago
0
allVariants.pe_sr, pu header formatting
#79
kunalkathuria
closed
6 years ago
0
Header for final bedpe file
#78
kunalkathuria
closed
6 years ago
0
Make SVLEN negative in INS_C DEL event
#77
kunalkathuria
closed
6 years ago
0
Calculate median covg for good regions only
#76
kunalkathuria
closed
6 years ago
0
Speed up chrHash formation in covPU by adding chunks at a time into hash table
#75
kunalkathuria
closed
6 years ago
0
2 semicolons in vcf output between groupid and support
#74
kunalkathuria
closed
6 years ago
0
cluster_c.r_orient string in de novo INS check
#73
kunalkathuria
closed
6 years ago
0
Implement "*chr" ignore for SRs also
#72
kunalkathuria
closed
6 years ago
0
Check if deletion thresholds etc. are best values
#71
kunalkathuria
closed
6 years ago
2
Pen perc can be a fxn of IL std if necessary
#70
kunalkathuria
closed
6 years ago
1
With all code changes, try non-dynamic support thresh = 4.
#69
kunalkathuria
closed
6 years ago
0
SPLIT_INS doesn't seem to add any gains to real data.
#68
kunalkathuria
closed
4 years ago
2
Confirm BND notation OK for INS/INS_I
#67
kunalkathuria
closed
6 years ago
0
Reasses/revise use of deletion threshold in PU for lower coverages
#66
kunalkathuria
closed
5 years ago
2
Temporary files for unsorted (name) discordant.bam are written in current dir, not in workspace
#65
kunalkathuria
closed
6 years ago
1
Update INS_C to INS_C_P with SR using swap
#64
kunalkathuria
closed
6 years ago
1
Notes for run-time for sims and real-data
#63
kunalkathuria
closed
4 years ago
8
Write same GROUP_ID for INS_C BND events as we know it's a translocation
#62
kunalkathuria
closed
6 years ago
1
Write all constants at front end in logging.info
#61
kunalkathuria
closed
6 years ago
0
Write precise sequence before and after for all SVs
#60
kunalkathuria
opened
6 years ago
0
Check if fragment supports final variants uniquely
#59
kunalkathuria
closed
5 years ago
1
SR cut-paste breakpoint update issue
#58
kunalkathuria
closed
6 years ago
0
Write INS events below size thresh as BNDs
#57
kunalkathuria
closed
6 years ago
1
INS_C_P SR calls too small/ why PE call went away
#56
kunalkathuria
closed
6 years ago
0
Write INS_C BNDs according to exact breakpoint support
#55
kunalkathuria
closed
6 years ago
0
In allVariants.pe_Sr.txt, separate cluster and frag support
#54
kunalkathuria
closed
6 years ago
0
Test branch
#53
kunalkathuria
closed
4 years ago
1
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