NBISweden/vcf2cytosure issues and pull requests

#62 - workflow for publishing...

Pull Request - State: closed - Opened by dnil 12 months ago

#61 - Fix #60 - exclude list to exclude also probes

Pull Request - State: closed - Opened by dnil about 1 year ago - 1 comment

#60 - Exclude list (blacklist) also affects probes

Issue - State: closed - Opened by dnil about 1 year ago

#59 - Make setup read version

Pull Request - State: closed - Opened by dnil over 1 year ago - 1 comment

#58 - Multiple probes "bleeding down" giving many small false positive deletions

Issue - State: open - Opened by dnil over 1 year ago - 1 comment

#57 - Not able to open .cgh file after saving it in Cytosure

Issue - State: open - Opened by mariapett about 2 years ago - 3 comments

#56 - v0.8 - continued: add Dockerfile

Pull Request - State: closed - Opened by dnil about 2 years ago

#55 - Fix log2 cov

Pull Request - State: closed - Opened by dnil about 2 years ago - 2 comments

#54 - Fix #53 - Ignore SV subtype

Pull Request - State: closed - Opened by dnil over 2 years ago - 2 comments

#53 - Error converting TIDDIT SVs

Issue - State: closed - Opened by khurrammaqbool over 2 years ago - 1 comment
Labels: bug

#52 - Support multiple cnvkit versions

Pull Request - State: closed - Opened by J35P312 over 2 years ago

#51 - Invert the CNV kit probes

Pull Request - State: closed - Opened by J35P312 over 2 years ago

#50 - Template genome - add hg38

Pull Request - State: closed - Opened by dnil over 2 years ago - 2 comments

#49 - Extend warning for multiple coverage options

Pull Request - State: closed - Opened by dnil over 2 years ago - 1 comment

#48 - Added support for cnvkit

Pull Request - State: closed - Opened by J35P312 over 2 years ago

#47 - Remaining dels in centromere region after clearing variant events in cytosure?

Issue - State: open - Opened by dnil over 3 years ago - 2 comments

#46 - Trouble re-opening saved cgh file in cytosure?

Issue - State: closed - Opened by dnil over 3 years ago
Labels: question

#45 - A sample name in the VCF overrides file name for sample id.

Pull Request - State: closed - Opened by dnil over 4 years ago - 1 comment

#44 - Update Singularity..

Pull Request - State: closed - Opened by dnil over 4 years ago

#43 - Generalise singularity...

Issue - State: closed - Opened by dnil over 4 years ago - 3 comments
Labels: enhancement

#42 - Fix #20: log version on run - also bump version.

Pull Request - State: closed - Opened by dnil over 4 years ago

#41 - Fix #37: M/M norm shows low probe heights on sex chr.

Pull Request - State: closed - Opened by dnil over 4 years ago

#40 - Blacklist

Pull Request - State: closed - Opened by dnil over 4 years ago - 1 comment

#39 - Blacklist for vcf2cytosure

Issue - State: closed - Opened by dnil almost 5 years ago
Labels: enhancement

#38 - Singularity

Pull Request - State: closed - Opened by J35P312 almost 5 years ago

#37 - M / M hyb shows too low coverage on X and Y? Factor?

Issue - State: closed - Opened by dnil over 5 years ago

#36 - zygosity

Issue - State: closed - Opened by dnil over 5 years ago - 1 comment
Labels: question

#35 - design file

Issue - State: closed - Opened by LaurensHannes over 5 years ago - 2 comments
Labels: enhancement

#34 - Hijack B-allelefreq plot?

Issue - State: open - Opened by dnil over 5 years ago
Labels: enhancement, Future plans

#33 - the zeroth element

Pull Request - State: closed - Opened by J35P312 over 5 years ago

#32 - Update .travis.yml

Pull Request - State: closed - Opened by dnil almost 6 years ago

#31 - Unsexy bugfixes!

Pull Request - State: closed - Opened by J35P312 almost 6 years ago

#30 - Sex option

Pull Request - State: closed - Opened by dnil almost 6 years ago

#29 - How jesper stole Christmas

Pull Request - State: closed - Opened by J35P312 almost 6 years ago - 5 comments

#28 - The height of the probes

Issue - State: closed - Opened by J35P312 over 6 years ago - 1 comment

#27 - Fix travis

Pull Request - State: closed - Opened by dnil over 6 years ago - 2 comments

#26 - Create requirements.txt

Pull Request - State: closed - Opened by dnil over 6 years ago - 1 comment

#25 - Add sample FindSV and MIP VCFs for testing

Issue - State: closed - Opened by dnil over 6 years ago - 3 comments

#24 - IDUP visualisation

Issue - State: closed - Opened by dnil over 6 years ago - 1 comment

#23 - CSQ field not exported to comment for all vcf files?

Issue - State: open - Opened by dnil over 6 years ago
Labels: question

#22 - Sex for reference sample should be changeable (set from command line)

Issue - State: closed - Opened by dnil over 6 years ago - 2 comments

#21 - Set sample ID from filename (or parameter if need b e)

Issue - State: closed - Opened by dnil over 6 years ago - 3 comments

#20 - Add version to output

Issue - State: closed - Opened by henrikstranneheim over 6 years ago - 3 comments
Labels: enhancement

#19 - visualise probe height using snv vcf

Pull Request - State: closed - Opened by J35P312 over 6 years ago - 13 comments

#18 - Merry christmas!

Pull Request - State: closed - Opened by J35P312 almost 7 years ago

#17 - Pull request!

Pull Request - State: closed - Opened by J35P312 almost 7 years ago

#16 - Handle MIP (from v5) VCF files

Issue - State: closed - Opened by dnil almost 7 years ago - 5 comments

#15 - Remove probes on centromeres

Issue - State: closed - Opened by marcelm about 7 years ago - 1 comment

#14 - Remove probes on short arms of certain chromosomes

Issue - State: closed - Opened by marcelm about 7 years ago