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cancerit
/
CaVEMan
SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
http://cancerit.github.io/CaVEMan
GNU Affero General Public License v3.0
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WIP: Fixes #74
#75
keiranmraine
closed
6 years ago
2
Split bug (sparse data edge-case)
#74
keiranmraine
closed
6 years ago
3
Correct estep.c help docs. WGX -> WXS. Fixes #61
#73
ghost
closed
6 years ago
1
Fixes #64
#72
ghost
closed
6 years ago
1
Fixes #65
#71
ghost
closed
6 years ago
1
error in caveman estep 1.12.0
#70
Sdgr90
closed
7 years ago
11
Feature/io improvements
#69
ghost
closed
7 years ago
1
Fail to parse output VCF files due to invalid UTF-8
#68
kevinrue
closed
7 years ago
3
Fast gzip compress estep snps/muts VCFs to reduce I/O & tmp footprint
#67
keiranmraine
closed
7 years ago
3
mstep - covs arrays could be optimised to reduce I/O for little CPU cost
#66
keiranmraine
closed
7 years ago
0
split.c - cli options parsed but never used
#65
keiranmraine
closed
6 years ago
2
bam_access_get_avg_readlength_from_bam: doesn't filter out sec/supp reads
#64
keiranmraine
closed
6 years ago
0
Incorrect genotype sorting in SNP calls
#63
ghost
opened
7 years ago
0
Error opening file to read cov array
#62
suimye
closed
7 years ago
2
estep help for options -l and -r
#61
sfbrunner
closed
6 years ago
1
CAVEMAN: Somatic Calls in SNPs File
#60
vyellapa
closed
7 years ago
2
caveman mstep with error: split_access_get_section_from_indexv Error opening split list file.
#59
dongqing7
closed
7 years ago
2
Feature/speed pileup upgrade
#58
ghost
closed
7 years ago
0
mergeCavemanResults
#57
ramaniak
closed
7 years ago
8
ERROR of esteps in 1.10.0
#56
kaji331
closed
7 years ago
2
Feature/check write flush covs
#55
ghost
closed
8 years ago
1
Added checks to flush and close files in covs_access.c
#54
ghost
closed
8 years ago
0
any best practices for RNA-seq SNV calling?
#53
davidroberson
closed
8 years ago
1
can --ignore-regions-file flag be used to ignore all but the chromosome of interest?
#52
davidroberson
closed
8 years ago
3
Feature/ci
#51
ghost
closed
8 years ago
0
Feature/travis ci
#50
ghost
closed
8 years ago
0
Merge hotfix into feature branch
#49
keiranmraine
closed
8 years ago
0
Feature/um panel strand info
#48
ghost
closed
8 years ago
0
Unmatched platforms result in an error but not an exit.
#47
ghost
closed
8 years ago
2
Install scripts in a cleaner way
#46
keiranmraine
closed
8 years ago
0
specifying external htslib
#45
ink1
closed
8 years ago
0
Feature/commandline entry checks
#44
ghost
closed
8 years ago
0
Feature/read length dependent split
#43
ghost
closed
8 years ago
0
Error with caveman setup command
#42
rdbcasillas
closed
9 years ago
3
generateCavemanUMNormVCF - Unmatched VCF generation errors
#41
ghost
closed
9 years ago
0
no calls gives unusual file sets
#40
keiranmraine
opened
9 years ago
2
Feature/merge with counts
#39
ghost
closed
9 years ago
0
High number of lanes causes error in merge
#38
ghost
closed
9 years ago
0
Copy number file defaults
#37
DaGaMs
closed
9 years ago
0
Crash when encountering a "bad" read
#36
DaGaMs
closed
9 years ago
8
generateCavemanUMNormVCF - get sample names from BAM header
#35
keiranmraine
opened
9 years ago
0
check BAM headers in setup for readgroups
#34
keiranmraine
closed
8 years ago
1
setup script doesn't install perl scripts
#33
ghost
closed
8 years ago
0
Bugfix to alg bean reader
#32
ghost
closed
9 years ago
0
Feature/cram support
#31
ghost
closed
9 years ago
3
Improve makefile for cram
#30
ghost
closed
9 years ago
1
Made SQ line parsing more robust
#29
ghost
closed
9 years ago
0
generateCavemanUMNormVCF - command line help has errors
#28
keiranmraine
closed
8 years ago
1
Generic unrolled lists
#27
pcostanza
closed
1 week ago
0
Merge 1.5.1 pre release code to master for a full release
#26
ghost
closed
10 years ago
0
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