gatk

gatk copied to clipboard

## Bug Report ### Affected tool(s) or class(es) VariantAnnotator ### Affected version(s) - [x] Latest public release version 4.5.0.0 - [ ] Latest master branch as of [date of test?]...

ykcchong

test run (was aborted after changed logic ran successfully): https://app.terra.bio/#workspaces/gvs-dev/RSA%20-%20GVS%20Quickstart%20V2%20/job_history/ed86ae93-41e7-4487-b8b1-3fc184bc64c3

rsasch

test run: https://app.terra.bio/#workspaces/gvs-dev/RSA%20-%20GVS%20Quickstart%20V2%20/job_history/52f8169b-f3b4-4145-a977-7a1e5dc3d807

rsasch

gbggrant

[bug report] CNNScoreVariants can't continue

1

## Bug Report I run the CNNScoreVariants as tutorial, but it can't continue and always stuck as the following picture, and the programme isn't stop by any error. By the...

Ithinky

gbggrant

About DP4

1

Hi， I use gatk HaplotypeCaller for variants calling, and I hope the generated vcf file can contain information about DP4. I wonder if there are parameters or other methods to...

Miles-TANGsk

ilyasoifer

Funcotator - removing the required transcript file

9

This PR removes the requirement for Gencode datasources to have transcript files. This is the first step in fixing some long-standing funcotator issues involving variants that run over the edge...

jonn-smith

several genes are reported in "PREDICTED_LOF" for a balanced translocation

3

**bug report** I have a balanced translocation (CTX) case and it has several genes (475 genes) under PREDICTED_LOF. However, one CTX breakpoint hits an intron of a gene, whereas the...

Nehir291