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40 Open 26 Closed
40 Open 26 Closed
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Issues list

Java Null Pointer Exception while running annotator with Docker
#283 opened Jul 12, 2024 by grabnervan
1
Error report misses '/' in URL column
#278 opened Apr 2, 2024 by leexgh
Singularity 3.7 got LinkageError when running master
#277 opened Apr 1, 2024 by leexgh
Singularity 3.3 cannot pull master docker
#276 opened Apr 1, 2024 by leexgh
Documentation for application.properties overrides via ENV variables enhancement genome-nexus good first issue
#275 opened Mar 25, 2024 by hweej
Handling Intergenic Variants in the MAF: Annotation Pipeline doesn't fill out any columns when VEP returns no transcript
#274 opened Feb 14, 2024 by rmadupuri
Error when having duplicated variants and no end positions
#271 opened Jan 17, 2024 by leexgh
Tumor_Seq_Allele1 and Tumor_Seq_Allele2 should be the same
#268 opened Oct 10, 2023 by leexgh
Add command parameter groups
#266 opened Sep 19, 2023 by leexgh
entrypoint to cmd switch breaks old usage of cli
#262 opened Sep 6, 2023 by inodb
2 tasks
Handling variants with common prefixes between GENIE and public GN
#260 opened Aug 21, 2023 by rmadupuri
1
Some complex variants with common prefix - suffix fail the annotation
#259 opened Aug 21, 2023 by rmadupuri
Add a new command parameter to set oncokb token
#254 opened Aug 8, 2023 by leexgh
CTNNB1 annotation fails but direct genome nexus API call succeed
#248 opened Jun 22, 2023 by leexgh
Add new flag for logging verbosity and log output location
#247 opened Jun 15, 2023 by leexgh
2
test failures building the project annotationPipeline
#243 opened Mar 23, 2023 by ldelgado-serrano
1
Improve dockerhub documentation
#237 opened Dec 23, 2022 by pieterlukasse
Add more versions in MAF header enhancement
#218 opened Aug 19, 2022 by inodb
1
Annotate big mutation file w/o failure
#216 opened Aug 16, 2022 by inodb
4
documentation for MAF formats
#215 opened Aug 16, 2022 by jagnathan
Minimal Output format is similar to TCGA bug
#210 opened Aug 9, 2022 by inodb
Account for Genome Nexus Timeout issue - check if all the variants in the MAF are annotated
#206 opened Jul 26, 2022 by rmadupuri
genome nexus tests to support both hg19 and hg38
#205 opened Jul 26, 2022 by jagnathan
3
Use subcommands for command line interface enhancement
#201 opened Jul 19, 2022 by inodb
Custom output format files
#194 opened Jun 14, 2022 by inodb
4 tasks
2
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