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cancerit
/
cgpPindel
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
http://cancerit.github.io/cgpPindel/
GNU Affero General Public License v3.0
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VCF - Mismatch AS/SP in headers doesn't fall back
#62
keiranmraine
closed
5 years ago
4
WIP: Improve input run time, specifically an issue for GRCh38
#61
keiranmraine
closed
5 years ago
1
Switch out bamcollate for samtools fast paired collate
#60
keiranmraine
opened
6 years ago
0
Feature/reads vs fragments
#59
keiranmraine
closed
6 years ago
0
When installing,t/1_pm_compile.t throws test error!
#58
0x1orz
closed
6 years ago
1
Feature/Add Dockerfile and improve README and INSTALL
#57
jsmedmar
closed
6 years ago
1
Pre-release tag for fragment analysis
#56
keiranmraine
closed
6 years ago
0
Compress intermediate sam files
#55
keiranmraine
closed
6 years ago
2
Calling InDel with only tumor sample
#54
tenglaowu
closed
7 years ago
1
VCF sorting
#53
keiranmraine
closed
7 years ago
1
VCF flag order
#52
keiranmraine
closed
7 years ago
0
VCF header - unstable ordering of contigs
#51
keiranmraine
opened
7 years ago
0
lsof failed to start
#50
jb-adams
closed
7 years ago
1
ifstream created with NULL value
#49
ezzymn
closed
7 years ago
0
Feature/reduce tmp space
#48
keiranmraine
closed
7 years ago
0
Feature/travis
#47
keiranmraine
closed
8 years ago
0
Problem in compiling cgpPindel
#46
GKerdivel
closed
8 years ago
15
pindel.pl - option apid incorrect capture type
#45
keiranmraine
closed
8 years ago
0
pindel_to_vcf - symlinks
#44
keiranmraine
closed
8 years ago
0
Feature/legacy htslib removal
#43
keiranmraine
closed
8 years ago
0
PindelRecordParser - investigate accurate VAF
#42
keiranmraine
opened
8 years ago
1
remove use of core 'constant' and replace with Const::Fast
#41
keiranmraine
closed
6 years ago
0
pindel_merge_vcf_bam.pl fails when SAM outputf have no records
#40
keiranmraine
closed
9 years ago
0
input generation fails when readgroup id = 0
#39
keiranmraine
closed
9 years ago
0
Ensure paths are absolute
#38
keiranmraine
closed
9 years ago
0
Fixes for analysisId into master
#37
keiranmraine
closed
9 years ago
0
cgpAnalysisProc - expose arg to top level script
#36
keiranmraine
closed
9 years ago
0
pindel_merge_vcf_bam.pl - Argument list too long
#35
keiranmraine
closed
9 years ago
1
Bamsort with no tmp space defined
#34
keiranmraine
closed
9 years ago
0
Typos in VCF headers
#33
keiranmraine
closed
9 years ago
0
Fix error in limit based indicies, bumped version for immediate release
#32
keiranmraine
closed
9 years ago
0
germline.bed - run bedtools merge to condense
#31
keiranmraine
closed
6 years ago
5
Corrected version number
#30
keiranmraine
closed
9 years ago
0
Modified behaviour for commandline assembly and species.
#29
ghost
closed
9 years ago
0
merge feature/1.2.0
#28
keiranmraine
closed
9 years ago
0
Feature/1.2.0
#27
keiranmraine
closed
9 years ago
0
bad path munging
#26
keiranmraine
closed
9 years ago
0
Master
#25
keiranmraine
closed
10 years ago
0
Fixes for install and test warnings
#24
keiranmraine
closed
10 years ago
1
threads wern't being honored when using process/index, bump version
#23
keiranmraine
closed
10 years ago
0
Ready for Pancancer
#22
keiranmraine
closed
10 years ago
0
Silly mistake in unlink
#21
keiranmraine
closed
10 years ago
0
Pre-release 1.0.3
#20
keiranmraine
closed
10 years ago
0
Cleanup output location
#19
keiranmraine
closed
10 years ago
0
1.0 bugfix i16 17
#18
keiranmraine
closed
10 years ago
0
input step tries to run with 0 threads
#17
keiranmraine
closed
10 years ago
0
List::MoreUtils needed in Makefile.PL
#16
keiranmraine
closed
10 years ago
0
Minor fix to readgroup id parsing
#15
keiranmraine
closed
10 years ago
0
Need to get absolute paths
#14
keiranmraine
closed
10 years ago
1
v1.0.1 missing executables on install
#13
keiranmraine
closed
10 years ago
0
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