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Dear Developers, I have been running CNNScoreVariants 2D on a single human sample (vcf from haplotype caller). Its been over a week and its still running. Is the any way...

vappiah

## Bug Report ### Affected tool(s) or class(es) MarkDuplicatesSpark ### Affected version(s) - Latest public release version [4.4.0.0] ### Description I am working on 40X human WGS data, running MarkDuplicatesSpark...

Han-Cao

SplitNCigarReads error - Attempt to add record to closed writer

1

Hi All, ### Affected tool(s) or class(es) gatk SplitNCigarReads ### Affected version(s) Version 4.2.5.0 I'm having a issue with running SplitNCigarReads on my local cluster. When I try to run...

ValerieCrolley

Please find attached samtools stats file. sample1.markdup.sorted.stats is before BQSR and ApplyBQSR sample1.stats is after BQSR and ApplyBQSR As you can see, before ApplyBQSR (NA12878-P.markdup.sorted.stats.txt), the raw total sequences is...

nathanLauHKGI

CNNScoreVariants crashes with java.lang.NullPointerException

5

Looks like this java.lang.NullPointerException is from an environment set up issue. This request was created from a contribution made by Jordi Maggi on April 25, 2022 09:25 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/5574426055963-CNNScoreVariants-crashes-with-java-lang-NullPointerException](https://gatk.broadinstitute.org/hc/en-us/community/posts/5574426055963-CNNScoreVariants-crashes-with-java-lang-NullPointerException)...

GATKSupportTeam

GATK 4.1.4 for joint calling of hifi and illumina reads

2

Hello, I am trying to use gatk/4.1.4.1 and picard/2.22.0 to do joint variant calling of PacBio HiFi reads and Illumina short-reads. My pipeline is basically the recommended one (without base...

YanisChrys

Embedded tags in javadoc are not rendered correctly in either javadoc or gatkdoc.

1

Original report by @samuelklee (see https://github.com/broadinstitute/barclay/issues/189): > I noticed that Javadoc @value tags are not being rendered correctly in e.g. https://gatk.broadinstitute.org/hc/en-us/articles/9570326304155-ScoreVariantAnnotations-BETA-. I used these tags to specify the variables corresponding...

cmnbroad

- Complex (CPX) SV records no longer use `END2`/`CHR2` INFO fields and instead are defined by `CPX_INTERVALS` in addition to normal coordinates. - Adds new class `SVCallRecord.ComplexEventInterval` for storing complex...

mwalker174

I need a PON vcf

3

Thanks a lot I am trying to run `mutect2` in **tumour-only** mode for which I need a panel of normal (PON) I have tried **somatic-hg38_1000g_pon.hg38.vcf.vcf** which gives `./gatk Mutect2 -R...

fi1d18

funcotator hg19 database 1.6 vs 1.7 - EGFR annotated with wrong ENST in 1.7 , but correct in 1.6

5

Dear *, I just updated the funcotator database for hg19 from 1.6 to 1.7. Here I observed for EGFR a wrong ENST assignment. I wanted funcotator to use ENST00000275493, which...

DanielAmsel