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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
Parameterized subprocesses and POD --help/--man changes.
#283 by alanhoyle was closed Apr 26, 2021 Loading… updated Apr 27, 2021
4
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
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
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
added tmp-dir option for vcf2maf.pl to control vep output
#85 by adamstruck was merged Oct 14, 2016 Loading… updated Feb 27, 2018
@ckandoth
1
vcf2maf with VEP latest version
#143 by alezanalp was closed Feb 27, 2018 Loading… updated Feb 27, 2018
@ckandoth
2
Add new test for MAF
#157 by inodb was closed Feb 26, 2018 Loading… updated Feb 26, 2018
@ckandoth
1
updated transcript for ASXL2
#127 by jjgao was merged Aug 7, 2017 Loading… updated Aug 7, 2017
@ckandoth @jjgao @aijazsyed
3
fix #118
#119 by raylim was closed May 2, 2017 Loading… updated May 2, 2017
@ckandoth
1
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