genome-nexus annotation-tools issues

genome-nexus / annotation-tools

Tools developed for AACR GENIE to allow annotation of vcf and maf files from a number of centers and merging the results

MIT License

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issues

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Automating Trust Store Update

#65 averyniceday opened 1 month ago
0
Blank FAILURE_REASONs

#64 Chelsea-Na opened 3 months ago
0
Add Java to Dockerfile to enable bash wrapper

#63 rmadupuri closed 4 months ago
1
Updates to dockerfile

#62 rmadupuri closed 6 months ago
0
Add initial github action for dockerhub build push

#61 hweej closed 6 months ago
0
[GEN-1026] Output annotation error report

#60 rxu17 closed 8 months ago
1
Unknown annotation failures reasons

#59 Chelsea-Na closed 3 months ago
1
vcf2maf not converting missing AD values to 0

#58 edoyango opened 12 months ago
0
Variant annotation failing

#57 Chelsea-Na opened 1 year ago
1
Add procps for ps command inside docker container

#56 hweej opened 1 year ago
0
Missing reference and variant allele

#55 Chelsea-Na closed 1 year ago
0
Fix Strelka type conversion issue

#54 rmadupuri closed 1 year ago
0
Add missing function that prints warnings for problematic files

#53 rmadupuri closed 1 year ago
0
Fix variant start position for Insertions

#52 rmadupuri closed 1 year ago
1
vcf2maf and maf2maf python tools

#51 rmadupuri closed 1 year ago
1
vcf2maf python tool

#50 rmadupuri closed 1 year ago
2
Dockerize annotation tools

#49 ruslan-forostianov closed 1 year ago
3
Improve tumor / nomal sample column detection in vcf files

#48 ruslan-forostianov closed 1 year ago
0
Improve tumor vs normal sample recognition in a vcf file

#47 ruslan-forostianov opened 1 year ago
4
Improvements to documentation and scripts

#46 ruslan-forostianov closed 1 year ago
7
declare read depth dict before use

#45 ao508 closed 2 years ago
0
java.net.UnknownServiceException

#44 marianakhoul opened 3 years ago
0
Several annotations show up as MUTATED in GENIE

#43 inodb opened 3 years ago
3
Attempt to fix #41

#42 inodb closed 3 years ago
1
Should not require VCF's to have `AF`

#41 thomasyu888 closed 3 years ago
0
Add minimal example to repo for testing

#40 inodb opened 3 years ago
0
Handle common prefixes in variant alleles

#39 ao508 closed 3 years ago
2
Fail early on incorrect variants

#38 inodb opened 3 years ago
0
Missing gnomAD values for particular variant

#37 thomasyu888 opened 3 years ago
3
Expand VCF allele count calculation method

#36 ao508 closed 3 years ago
1
Annotation tools doesn't calculate t_ref_count and t_alt_count from particular site's VCF field

#35 thomasyu888 closed 3 years ago
5
Genome Nexus: 41 variants that have incorrectly annotated ref/alt.

#34 thomasyu888 closed 3 years ago
10
Genome Nexus sometimes annotates SNV as ONP

#33 thomasyu888 opened 3 years ago
4
Genome Nexus sometimes annotates SNV as DNP

#32 thomasyu888 opened 3 years ago
5
Genome Nexus creates variants with Reference_Allele == Tumor_Seq_Allele2 == Tumor_Seq_Allele1

#31 thomasyu888 opened 3 years ago
8
Genome Nexus changes the Reference Allele and Tumor_Seq_Allele2

#30 thomasyu888 closed 3 years ago
7
Genes referred to by both their approved and previous name

#29 thomasyu888 closed 3 years ago
6
Add missing component to gnomAD overlay tool

#28 sheridancbio closed 3 years ago
0
Python script to overlay gnomAD values on MAF

#27 sheridancbio closed 3 years ago
0
How does Genome Nexus handle Tumor Seq Allele1 and Tumor Seq Allele2

#26 thomasyu888 closed 3 years ago
11
Fix bug in resolving tumor seq allele 1 value

#25 ao508 closed 4 years ago
0
Additional non-standard MAF support

#24 ao508 closed 4 years ago
0
Report logs/warnings/errors encountered during MAF standardization run

#23 ao508 opened 4 years ago
0
Handle UnicodeDecodeError when reading data files

#22 ao508 closed 4 years ago
2
some vcfs have non-ascii characters

#21 thomasyu888 closed 4 years ago
0
How to properly handle variants that can't be annotated?

#20 thomasyu888 closed 4 years ago
6
Resolve tumor seq alleles independently from each other

#19 ao508 closed 4 years ago
0
MAF files that had missing column headers fail GenomeNexus annotation

#18 thomasyu888 closed 4 years ago
1
Hotfix

#17 ao508 closed 4 years ago
0
Resolve normal seq allele value error

#16 ao508 closed 4 years ago
1