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ReblockGVCF bug: first position on contig missing

2

## Bug Report ### Affected tool(s) or class(es) ReblockGVCF ### Affected version(s) - [x] Latest public release version [4.2.6.1] - [x] Latest master branch (probably) ### Description First position on...

ldgauthier

FilterMutectCalls when using --alleles yields java.lang.IllegalArgumentException: log10 p: Values must be non-infinite and non-NAN

5

## Bug Report This is more of a question than an outright bug report. Is it expected that `FilterMutectCalls` should work on a VCF produced by `Mutect2` run with the...

Ben-Habermeyer

Spark 3.3.0 - WIP.

39

cmnbroad

IllegalStateException in GenotypeGVCFs after GenomicsDBImport - GATK 4.2.6.1

9

### IllegalStateException in GenotypeGVCFs after GenomicsDBImport - GATK 4.2.6.1 Looks like there are similar issues occurring in #7639 and #7933. This is a follow up report from the GATK Forum....

AJDCiarla

Fixed the broken test in DirichletAlleleDepthAndFractionIntegrationTest

2

jamesemery

SVLEN missing from gCNV output

1

Hello, I am running GermlineCNVCaller and PostprocessGermlineCNVCalls (GATK v4.2.5) for CNV analysis on our targeted capture. My output segment vcfs have no SVLEN or SVTYPE values although those are described...

Addy81

No non variant sites

7

I use GenomicsDBImport to generate a GenomicsDB workspace, the parameter --include-non-variant-sites of GenotypeGVCFs has no effect.No non-variant sites were obtained.And the number of folders under --genomicsdb-workspace-path is less than the...

KPS-Malpe

clearer error when values are missing

1

In the VAT validation, give clearer error msg about which clinvar classification values are missing

RoriCremer

Mutect2 (and HaplotypeCaller) version 4.1.3.0 miscounts number of alleles when overlapping reads are present, as if the "--count-reads" was set to true by default

13

I obtain this reproducible issue with gatk 4.1.3.0: First of all, you have to download the mini input.bam file from this dropbox link: https://www.dropbox.com/sh/78rz5wrhu9zkfzh/AACW9ZPhl4WnD-wmAkKcdHT3a?dl=0 Then setup a GATK working environment:...

freeseek

(DO NOT MERGE) Draft PR for reimplementation of annotation-based filtering tools.

6

samuelklee