SvAnna

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Error Reading gencode.v38.genes.json.gz File in SvAnna CLI Tool

7

Hello, I am experiencing an issue while running the SvAnna CLI tool. I receive the following error message when executing the command: ERROR o.m.svanna.cli.cmd.PrioritizeCommand - Error: Error reading genes from...

pragnapcu

feature request: processing of vcs from Delly

1

Hi there, We would like to process vcf outputs from the caller Delly with SvAnna, if possible. Below is a subset of the errors we encounter: _____ ___ / ___/_...

jessmewald

Compatibility with phased assembly variant caller?

8

Hi there, thanks for developing such an easy to use tool. We would like to run SvAnna with VCF outputs from PAV. It seems that SvAnna is truncating the vcfs...

jessmewald

Bumps [guava](https://github.com/google/guava) from 31.1-jre to 32.0.0-jre. Release notes Sourced from guava's releases. 32.0.0 Maven <dependency> <groupId>com.google.guava</groupId> <artifactId>guava</artifactId> <version>32.0.0-jre</version> <!-- or, for Android: --> <version>32.0.0-android</version> </dependency> Jar files 32.0.0-jre.jar 32.0.0-android.jar Guava...

dependabot[bot]

Hi, Thank you for creating and maintaining this really useful tool! I was wondering whether there is also tabular output for which gene and genomic region (eg. Promoter, enhancer, etc.)...

kerstinth

Bumps commons-net from 3.8.0 to 3.9.0. [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a...

dependabot[bot]

Hi, now I plan to use this tool to output annotation of vcf of SV which related gene and transcript, but it seems to have no separate command line to...

Overinterested

294 kb insertion within the coding sequence of CCM2

2

https://pubmed.ncbi.nlm.nih.gov/32286434/ How would we annotate this in HCA?

pnrobinson

Let's support both _Gencode_ and _RefSeq_ transcripts, and allow to limit the analysis to high-confidence _RefSeq _ transcripts only.

ielis

https://pubmed.ncbi.nlm.nih.gov/26163108/

pnrobinson