Skip to content

Pull requests: mskcc/vcf2maf

New pull request New
Clear current search query, filters, and sorts
1 Open 44 Closed
1 Open 44 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

Add snpeff annotation
#363 by kmavrommatis was merged Dec 9, 2024 Loading… updated Dec 9, 2024
adding plugin parameter to vcf2maf
#357 by allaway was merged Dec 9, 2024 Loading… updated Dec 9, 2024
Remove deprecated VEP 110 argument
#350 by MatthijsPon was merged May 30, 2024 Loading… updated May 30, 2024
Remove --af_esp flag as it's deprecated
#324 by bozbezbozzel was merged May 30, 2024 Loading… updated May 30, 2024
@ckandoth
1
handle file names and paths which contain special characters
#331 by xnr13 was merged Nov 7, 2022 Loading… updated Nov 7, 2022
@ckandoth
1
Handle new splice effects in ensembl-vep version 105
#320 by GFJHogue was merged Nov 7, 2022 Loading… updated Nov 7, 2022
@ckandoth
1
Remove --af_esp for compatibility with v107 ensemble
#328 by allaway was closed Aug 26, 2022 Loading… updated Aug 26, 2022
1
vcf2maf.pl: --vep-stats to work around VEP bug
#318 by alanhoyle was merged Jun 29, 2022 Loading… updated Jun 29, 2022
4
POD changed, external exec params
#284 by alanhoyle was merged Apr 27, 2021 Loading… updated Apr 27, 2021
6
Parameterized subprocesses and POD --help/--man changes.
#283 by alanhoyle was closed Apr 26, 2021 Loading… updated Apr 27, 2021
4
Verbose mode, customizable VEP command and output
#282 by alanhoyle was merged Apr 23, 2021 Loading… updated Apr 23, 2021
5
Update isoform_overrides_at_mskcc
#271 by zhx828 was merged Oct 29, 2020 Loading… updated Nov 9, 2020
1
@ckandoth
3
Update isoform_overrides_uniprot
#270 by marianakhoul was merged Nov 6, 2020 Loading… updated Nov 6, 2020
Update the RECQL4 refseq id
#261 by zhx828 was merged Oct 26, 2020 Loading… updated Oct 26, 2020
1
VEP reports "lncRNA" "lincRNA" with different builds
#249 by alanhoyle was merged Jul 20, 2020 Loading… updated Jul 20, 2020
@ckandoth
1
New flag to skip VEP, but still extract VEP data if any
#248 by ckandoth was merged Apr 20, 2020 Loading… updated Jul 17, 2020
@ckandoth
2
add command line option --inhibit-vep
#246 by sheridancbio was merged Apr 17, 2020 Loading… updated Apr 17, 2020
@ckandoth
3
Feature/install vep in docker
#244 by caaespin was closed Feb 28, 2020 Loading… updated Feb 28, 2020
Update uniprot isoform for PLCG2 (grch37)
#225 by inodb was merged May 14, 2019 Loading… updated May 14, 2019
@ckandoth
1
Fixed handling of allele depths for Indels called by Strelka
#215 by sebastianlange was merged Mar 17, 2019 Loading… updated Mar 17, 2019
@ckandoth
2
Add gene NCOR2
#212 by zhx828 was merged Jan 25, 2019 Loading… updated Jan 25, 2019
@ckandoth
Add gene EP400
#188 by zhx828 was merged Aug 16, 2018 Loading… updated Aug 16, 2018
removed redundant mapping in uniprot_override
#164 by jjgao was merged Apr 4, 2018 Loading… updated Jul 26, 2018
1
fixed isoform assignment for HIST1H4A
#183 by jjgao was merged Jul 26, 2018 Loading… updated Jul 26, 2018
3
Update uniprot isoform list to only have biomart ensembl v91 genes
#166 by inodb was merged May 9, 2018 Loading… updated May 9, 2018
8
ProTip! Filter pull requests by the default branch with base:main.