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java.lang.IllegalStateException in JointGermlineCNVSegmentation

4

## Bug Report ### Affected tool(s) or class(es) JointGermlineCNVSegmentation ### Affected version(s) - [x] Latest public release version [v4.3.0.0] - [ ] Latest master branch as of [date of test?]...

holtgrewe

Issue #7159 Create tool for producing genomic regions (as a BED file)

2

Converts GTF files to BED file format with an option for gene or transcript level processing and an option to only use transcripts with basic tag

sanashah007

HaplotypeCaller is reporting DP in HOMREF region differently when ploidy is set to 1 with different Interval inputs

6

Hi all. This looks like an issue presented by a forum post [Haplotypecaller FORMAT:DP is affected by the interval in WGS](https://gatk.broadinstitute.org/hc/en-us/community/posts/27992393649051-Haplotypecaller-FORMAT-DP-is-affected-by-the-interval-in-WGS) User uploaded a toy data for us to test...

gokalpcelik

gbggrant

Not sure if this is a bug or something wrong with my bam files. Any help on solving/debugging would be welcomed. Running mutect2 returns >100,000 warnings of more than two...

ChrisSteel-bio

Funcotator: all Clinvar fields blank

3

Hi, With the latest version of gatk 4.6.0 and the latest funcotator v1.8 annotation, all Clinvar fields are returning blank, even though there are many variants that I know are...

gevro

Strange output by Funcotator

2

Hi, With gatk 4.6.0 and Funcotator data sources v1.8, and output in VCF format, I'm seeing some annotations with strange character combinations inside of them: "_%7C_" "_%20_" For example for...

gevro

Bundle support for FeatureInputs, references; add CreateBundle tool.

7

Draft until a release of htsjdk with https://github.com/samtools/htsjdk/pull/1702, https://github.com/samtools/htsjdk/pull/1703, and https://github.com/samtools/htsjdk/pull/1713 is available.

cmnbroad

Document provenance of GRCh38 resource files in GATK bundle

3

Folks occasionally but consistently ask for this information on the forum and our current answer is that we provide these files as is. For the new GATK4 documentation, which we...

sooheelee

VariantFiltration failed

2

Hello, I was trying to hard-filter the vcf files outputed by GATK HaplotypeCaller, and I want to keep variants that meet the following condition: depth (QD) < 2.0 || FisherStrand...

Wasya-the-Wolf