nmdp-bioinformatics pipeline issues

nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.

GNU Lesser General Public License v3.0

7 stars 7 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

V1.4.0

#131 mhalagan closed 8 years ago
0
fixed an issue with how the uuids were being loaded.

#130 mhalagan closed 8 years ago
0
Changed the way the experiments were being taken from the files.

#129 mhalagan closed 8 years ago
0
V1.3.5

#128 mhalagan closed 8 years ago
0
V1.3.4

#127 mhalagan closed 9 years ago
0
Rename the UUIDs

#126 mhalagan opened 9 years ago
0
V1.3.3

#125 mhalagan closed 9 years ago
0
Added zcat option for Linux machines and gzcat for macs.

#124 mhalagan closed 9 years ago
1
Added text testing file.

#123 mhalagan closed 9 years ago
1
V1.3.0

#122 mhalagan closed 9 years ago
1
Made a slight chagne with how the new observed format is being loaded.

#121 mhalagan closed 9 years ago
1
ngs-imgt-db

#120 mhalagan closed 9 years ago
1
V1.2.2

#119 mhalagan closed 9 years ago
1
Fixed issue that was caused by using different versions of perl! Adde…

#118 mhalagan closed 9 years ago
1
V1.2.0

#117 mhalagan closed 9 years ago
1
V1.1.1

#116 mhalagan closed 9 years ago
1
Package validation code and dependencies for installation to Docker

#115 ghost closed 9 years ago
0
Added bed reformatted versions of regions files

#114 ckennedy-nmdp closed 9 years ago
1
Update validation report

#113 mhalagan closed 9 years ago
1
Update report

#112 mhalagan closed 9 years ago
4
Consensus filtering

#111 ckennedy-nmdp closed 9 years ago
2
Separate DRB1 from DRB3,4,5 top hits

#110 ybolon-nmdp opened 9 years ago
0
Request to version the pipeline and coordinate with ngs-tools release and samtools release

#109 ybolon-nmdp opened 9 years ago
0
Updated pipeline/samtools combo produces empty vcf output

#108 ybolon-nmdp opened 9 years ago
2
Upgrade to samtools v1.1

#107 ckennedy-nmdp closed 9 years ago
2
Ngs validation report

#105 mhalagan closed 9 years ago
0
Interpretation validation should compare against allele codes and GL Strings

#104 ghost closed 9 years ago
1
Add genomic regions for KIR2DL1 gene features

#103 ckennedy-nmdp closed 9 years ago
2
Change reference variables to GRCh38 with no alternative assemblies

#102 ckennedy-nmdp closed 9 years ago
1
Add genomic coordinates for Dave's KIR-2DL1 gene features

#101 ckennedy-nmdp closed 9 years ago
2
Remove observed results, should be generated from smoke test

#100 ckennedy-nmdp closed 9 years ago
2
SSAKE should be installed from homebrew

#99 ghost closed 9 years ago
1
Use /opt/ngs-tool/ for default TOOLDIR

#98 ghost closed 9 years ago
1
Default TOOLDIR should be /opt/ngs-tools

#97 ghost closed 9 years ago
0
Add expected results

#96 ckennedy-nmdp closed 9 years ago
1
Removing crossvalidate.groovy, fixes #92

#95 ghost closed 9 years ago
1
Add compressed test data

#94 ckennedy-nmdp closed 9 years ago
1
Add raw test data

#93 ckennedy-nmdp closed 9 years ago
1
Deprecate crossvalidate.groovy for ngs-validate-interpretation

#92 ghost closed 9 years ago
1
Add regions and smoke-test configuration files to tutorial/

#91 ckennedy-nmdp closed 9 years ago
1
Removing splice-bam.groovy, fixes #89

#90 ghost closed 9 years ago
2
Deprecate splice-bam.groovy for ngs-filter-consensus

#89 ghost closed 9 years ago
0
Add cross-validation script

#88 ckennedy-nmdp closed 9 years ago
0
Add filtering and interpretation script

#87 ckennedy-nmdp closed 9 years ago
5
Remove soft-clipped sequences

#86 ckennedy-nmdp closed 9 years ago
0
Fix for DPB1 typo

#85 ghost closed 9 years ago
1
splice-bam.groovy must remove soft-clips in aligned contigs

#84 ckennedy-nmdp closed 9 years ago
1
Increasing mean coverage from 100x to 1500x

#83 ghost closed 9 years ago
1
Add option to filter consensus (cDNA) sequences by ouputting the first p...

#82 ckennedy-nmdp closed 9 years ago
0