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27 Open 7 Closed
27 Open 7 Closed
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Issues list

pipeline expects different format of *.bed.cov* files
#220 opened Feb 19, 2019 by marnec
Pipeline fails with VEP 95
#219 opened Feb 19, 2019 by marnec
links are dead
#218 opened Feb 15, 2019 by marnec
Not finding pre-existing VEP during install
#217 opened Oct 3, 2018 by tirohia
rerun with another BED file?
#216 opened Aug 14, 2018 by biocyberman
What replaced annovar?
#214 opened Jan 6, 2018 by biocyberman
2
How to prepare $DATA/annotation/1000Gp3.vcf.gz?
#213 opened Jan 6, 2018 by biocyberman
Fix metadata file validation
#212 opened Nov 15, 2017 by multimeric
numerous problems with installation
#210 opened Oct 27, 2017 by biocyberman
3
Information for maybe further tuning GATK parameters
#207 opened Apr 4, 2017 by biocyberman
Install without swift_credentials.sh ?
#206 opened Mar 1, 2017 by biocyberman
3
Self Test Script Fail - [samopen] no @SQ lines in the header.
#205 opened Feb 21, 2017 by stone84
Memory issue at VEP stage
#203 opened Jan 16, 2017 by RoxaneLS
Missing file /opt/cpipe/designs/ALL/generated_target_regions.bed
#196 opened Nov 21, 2016 by RoxaneLS
5
VEP install fails due to cvs.sanger.ac.uk not being online
#195 opened Nov 17, 2016 by stetner
1
provenance script
#125 opened Jun 9, 2016 by ramaniak
New design issue
#117 opened May 19, 2016 by ramaniak
4
Installer should prompt for site / pipeline id
#104 opened Feb 26, 2016 by ssadedin
Bad formatting in config.groovy is not well handled by install script
#91 opened Feb 11, 2016 by ssadedin
EOF header is absent
#76 opened Dec 18, 2015 by SarahBeecroft
1
Sample ID Longer than 30 Chars Causes Failures in Generation of Excel Reports
#23 opened May 22, 2015 by ssadedin
Add pipeline stage to create mini bams for each variant
#20 opened May 13, 2015 by supernifty
1
CARDIOM Integration test fails with default GATK
#19 opened May 13, 2015 by supernifty
Better handling for Perl dependencies
#16 opened May 7, 2015 by ssadedin
Warning about /tmp
#14 opened Apr 29, 2015 by hdashnow
ProTip! What’s not been updated in a month: updated:<2025-01-03.