MelbourneGenomics cpipe issues

MelbourneGenomics / cpipe

The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline

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issues

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pipeline expects different format of *.bed.cov* files

#220 marnec opened 5 years ago
0
Pipeline fails with VEP 95

#219 marnec opened 5 years ago
0
links are dead

#218 marnec opened 5 years ago
0
Not finding pre-existing VEP during install

#217 tirohia opened 6 years ago
0
rerun with another BED file?

#216 biocyberman opened 6 years ago
0
Fix race condition that makes multi-process installation fail

#215 biocyberman closed 6 years ago
1
What replaced annovar?

#214 biocyberman opened 6 years ago
2
How to prepare $DATA/annotation/1000Gp3.vcf.gz?

#213 biocyberman opened 6 years ago
0
Fix metadata file validation

#212 multimeric opened 6 years ago
0
Some bugfixes for the installation process

#211 biocyberman opened 6 years ago
0
numerous problems with installation

#210 biocyberman opened 6 years ago
3
Update master to dev (release 2.5.0)

#209 multimeric opened 7 years ago
0
Restructured cpipe directory, various other features

#208 multimeric closed 7 years ago
0
Information for maybe further tuning GATK parameters

#207 biocyberman opened 7 years ago
0
Install without swift_credentials.sh ?

#206 biocyberman opened 7 years ago
3
Self Test Script Fail - [samopen] no @SQ lines in the header.

#205 stone84 opened 7 years ago
0
fix 'bpipe test' always stops at first stage

#204 ssadedin closed 7 years ago
1
Memory issue at VEP stage

#203 RoxaneLS opened 7 years ago
0
additional dbnsfp fields, remove redundant exac/1000g fields

#202 supernifty closed 7 years ago
0
AF annotation

#201 supernifty closed 7 years ago
0
Installer fix

#200 multimeric closed 7 years ago
0
Fix installer bug being unable to remove temp dir

#199 multimeric closed 7 years ago
0
Convert Cpipe to Python 3

#198 multimeric closed 7 years ago
0
additional metadata field descriptions

#197 supernifty closed 7 years ago
0
Missing file /opt/cpipe/designs/ALL/generated_target_regions.bed

#196 RoxaneLS opened 7 years ago
5
VEP install fails due to cvs.sanger.ac.uk not being online

#195 stetner opened 7 years ago
1
warn and continue if a sample has additional columns in qc_report

#194 supernifty closed 7 years ago
0
Public installer

#193 multimeric closed 7 years ago
0
Fix manage batch unit tests

#192 multimeric closed 7 years ago
0
Upgrade 2.4

#191 multimeric closed 7 years ago
0
Install rewrite

#190 multimeric closed 7 years ago
0
Cpipe 2.4 Docker install issue

#189 RoxaneLS closed 7 years ago
35
Bpipe config branch PR

#188 multimeric closed 7 years ago
1
V2.4 xm filter

#187 multimeric closed 7 years ago
0
Apply XM filtering to final LOVD output

#186 supernifty closed 7 years ago
0
xm transcript filtering

#185 supernifty closed 8 years ago
0
XM filter issue184

#184 supernifty closed 8 years ago
0
generate all vep transcripts

#183 supernifty closed 8 years ago
0
parent analysis

#182 supernifty closed 8 years ago
0
analyse parents by default unless exclude is specified in pedigree_file

#181 supernifty closed 8 years ago
0
2.4

#180 multimeric closed 8 years ago
0
DBnsfp option (CPIPE-164)

#179 supernifty closed 8 years ago
1
2.3 updates

#178 supernifty closed 8 years ago
0
Style guide

#177 multimeric closed 8 years ago
1
Gap annotation column changes

#176 supernifty closed 8 years ago
1
add padding to all stages of pipeline CPIPE-173

#175 supernifty closed 8 years ago
1
workaround for centos bgfz bug (PIF-5)

#174 supernifty closed 8 years ago
0
fix failure generating provenance report with new bpipe

#173 ssadedin closed 8 years ago
0
fix lack of output variable breaking bpipe test / retry

#172 ssadedin closed 8 years ago
0
fix install from scratch broken

#171 ssadedin opened 8 years ago
0