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ICGC-TCGA-PanCancer
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PCAP-core
Legacy, see cancerit/PCAP-core: NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project
GNU General Public License v2.0
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removing link rot in setup.sh
#156
GentleInfant
opened
4 months ago
0
changing call to cpanm to use https version of site
#155
GentleInfant
closed
4 months ago
0
got this error when I install pcap-core
#154
NickyPan
closed
6 years ago
1
Add the ability to pass PL and LB tags to bwa_mem.pl to perform GTAK's best practices
#153
jsmedmar
closed
6 years ago
1
Installation Fail
#152
lmy06
closed
6 years ago
1
Compiling failed after installing prerequisite.
#151
carolinie36
opened
7 years ago
2
Add more testing related to PR145
#150
keiranmraine
closed
6 years ago
1
Feature/lsof check
#149
keiranmraine
closed
7 years ago
0
Feature/gnos rna
#148
keiranmraine
closed
7 years ago
0
Speedup BAM output, not directly compatible with CRAM
#147
keiranmraine
closed
7 years ago
0
found missing deps
#146
mcast
closed
7 years ago
3
Added diff_bams as a c program. 2hrs(perl)->45mins(c) for a 68G bam file
#145
ghost
closed
7 years ago
1
installation fail
#144
alkodsi
closed
7 years ago
8
setup.sh - fix /proc/cpuinfo so works on osx
#143
keiranmraine
closed
7 years ago
1
reheaderSQ - dies if @HD in dict
#142
keiranmraine
closed
7 years ago
0
Adds ability to switch out malloc and control threads in BWA mapping …
#141
keiranmraine
closed
8 years ago
0
WIP: Release/v3.2.0
#140
keiranmraine
closed
8 years ago
1
bwa_mem.pl - improve error message when no input files
#139
keiranmraine
closed
7 years ago
0
Attempted conversion to cgpBigWig
#138
keiranmraine
closed
8 years ago
2
Convert to cgpBigWig
#137
keiranmraine
closed
7 years ago
1
Feature/bam2bedgraph
#136
ghost
closed
8 years ago
0
Feature/update bam to bw
#135
keiranmraine
closed
8 years ago
0
bam2bedgraph implemented and added to c Makefile
#134
ghost
closed
8 years ago
0
bam2bedgraph - rework for HTSlib
#133
keiranmraine
closed
8 years ago
0
Feature/adapter trim
#132
keiranmraine
closed
8 years ago
0
Remove dependancy on Bio::DB::HTS INSTALL.pl
#131
keiranmraine
closed
8 years ago
1
Add travis-ci build
#130
keiranmraine
closed
8 years ago
1
Provide option for CRAM as output via scramble
#129
keiranmraine
closed
8 years ago
1
bwa version upgrade to 0.7.15
#128
keiranmraine
closed
8 years ago
1
bwa_mem.pl - genome.fa.gz handling
#127
keiranmraine
closed
8 years ago
1
bwa_mem.pl - drop '-T 0'
#126
keiranmraine
closed
8 years ago
1
INSTALL.md - remove libgd requirement
#125
keiranmraine
closed
8 years ago
0
bwa_mem.pl - add option for adaptor trimming
#124
keiranmraine
closed
8 years ago
1
Feature/log handling
#123
keiranmraine
closed
8 years ago
1
Add relevant tools generating extreme depth file from BigWig
#122
keiranmraine
closed
8 years ago
0
bamToBw.pl - Expose filter flag parameters
#121
keiranmraine
closed
8 years ago
0
Feature/fix big wig
#120
keiranmraine
closed
8 years ago
0
Feature/bwcat
#119
keiranmraine
closed
8 years ago
0
Added code to ignore files
#118
keiranmraine
closed
8 years ago
0
Added reheadSQ script and compilation instructions
#117
ghost
closed
8 years ago
9
Feature/bigwig cat
#116
ghost
closed
8 years ago
1
Feature/coverage
#115
ghost
closed
8 years ago
0
Feature/bam to hts
#114
keiranmraine
closed
8 years ago
0
Feature/no dup rem option
#113
keiranmraine
closed
8 years ago
0
bwa_mem.pl - Fails when input BAM(s) have orphan reads
#112
keiranmraine
closed
8 years ago
0
bwa_mem.pl - add no-dup-mark option
#111
keiranmraine
closed
8 years ago
0
Cram as input for BWA_mem.pl
#110
keiranmraine
closed
8 years ago
0
c_test: inconsistency in test output
#109
keiranmraine
closed
8 years ago
2
bam_stats (c) - tests fail when running as root
#108
keiranmraine
closed
8 years ago
0
Unused variables bam_stats(c)
#107
keiranmraine
closed
8 years ago
0
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