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SIGSEGV when running gatk/4.6.0.0

6

\* Opening on behalf of a user on an HPC cluster, my knowledge in this field is a bit limited. ### Affected tool(s) or class(es) gatk HaplotypeCaller ### Affected version(s)...

emwjacobson

Memory leak in GenotypeGVCFs with `-all-sites`

8

## Bug Report ### Affected tool(s) or class(es) GenotypeGVCFs with `-all-sites` ### Affected version(s) - 4.2 through 4.6 ### Description We tried to run GenotypeGVCFs from GATK 4.5 with `-all-sites`...

brisk022

Base-specific Phred score filtering/output options in AnalyzeSaturationMutagenesis

1

Hey there! I am currently working on a project involving mutagenesis analysis using the AnalyzeSaturationMutagenesis tool. Our rationale is that a single nucleotide exchange due to a sequencing error is...

BenjaminWehnert1008

Merging phased indels

2

We are performing somatic variant calling in tumour-only mode where we call variants with both Mutect2 (GATK version 4.1.2.0) and Vardict-java. We have noticed that Mutect2 calls adjacent phased indels...

asgerjakobsen

It would be nice if the `ProgressBar` had an additional column with an estimate of the time remaining for the tool.

jonn-smith

Implements two new tools and updates some methods for a revamp of the `CombineBatches` cross-batch integration module in [gatk-sv](https://github.com/broadinstitute/gatk-sv). - `SVStratify` - tool for splitting out a VCF by variant...

mwalker174

FlowFeatureMapper speed improvements

3

1. Allow for using separate threads for reading / processing / writing (max 3) 2. Use NM SAM tag instead of edit distance 3. Perform likelihood scoring on trimmed read...

dror27

Update VariantRecalibrator RScript Compatibility with Newer ggplot2 Versions

1

Hi, I've encountered an issue with the R script generated by `VariantRecalibrator` during my analysis. The generated R script uses color functions (`scale_fill_gradient`) where the RGB color space is still...

Nanderson246

Feature Request - extract Funcotator VCF INFO 'sub-fields'

3

A user on the GATK Forum submitted a request to make the INFO field easier to manipulate through creating a table. At the GATK Office Hours meeting 11/8, we discussed...

GATKSupportTeam

I know to how filter on whole info fields, but funcotations are subfields of the FUNCOTATION info field. So, how do I filter on, say, gnomAD_genome_AF.

keenhl