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Potential fix for code scanning alert no. 15: Implicit narrowing conversion in compound assignment

1

Potential fix for [https://github.com/broadinstitute/gatk/security/code-scanning/15](https://github.com/broadinstitute/gatk/security/code-scanning/15) To fix the problem, we need to change the type of the `total` variable from `int` to `long`. This will ensure that the sum of the...

lbergelson

MUTECT2: allow_potentially_misencoded_quality_scores argument is missing

1

According to the [documentation](https://gatk.broadinstitute.org/hc/en-us/articles/360035532312-Errors-about-misencoded-quality-scores) when we face problems with quality scores, we can disable the quality scores check. **It is impossible to use** GATK products for UMI processed bams from...

VasLem

Hi After running vcf-validator (https://github.com/EBIvariation/vcf-validator) for mutect2 vcf (gatk 4.6.1.0), warnings appear for INFO/AS_SB_TABLE, for example: `Line 243: INFO AS_SB_TABLE does not match the meta specification Number=1 (expected 1 value(s))....

jomoxi

GatherBamFiles Indexing Bug

8

Hi, I am testing GatherBamFiles of gatk-4.1.4.1 and gatk-4.1.2.0: when I set '--CREATE_INDEX false', the command goes well and the resulted bam could be indexed by samtools, however, when I...

gudeqing

Enabling PDHMM causes GVCF mode to fail.

5

Hi team. Enabling `--use-pdhmm true` for HaplotypeCaller results in the below error message thrown when `-ERC GVCF` is enabled. ``` java.lang.IllegalArgumentException: refHaplotype cannot be null at org.broadinstitute.hellbender.utils.Utils.nonNull(Utils.java:643) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.calculateRefConfidence(ReferenceConfidenceModel.java:216) at...

gokalpcelik

Mutect2 doesn't call SNP despite high coverage and strong evidence unless forced with --alleles

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Hi there, I'm using Mutect2 to call variants on amplicon sequencing data of human mitochondrial DNA. In one specific amplicon with a very clean signal and a read depth of...

PeterResutik

Update hadoop 3.3.6 -> 3.4.0

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lbergelson

RoriCremer

Hi there, Just wondering if there is a best-practice pipeline for calling somatic mutations using RNA-seq data. I noticed a discussion here: [https://gatk.broadinstitute.org/hc/en-us/community/posts/23387556065691-Somatic-and-germline-mutations-from-RNA-seq-data](https://gatk.broadinstitute.org/hc/en-us/community/posts/23387556065691-Somatic-and-germline-mutations-from-RNA-seq-data) and it says that `HaplotyeCaller` assumes a...

hukai916

GATK4.5.0.0 HaplotypeCaller exits with error code 245 while no error message

1

Greetings, I am trying to use hifi long reads identifying the SNVs, but I have noticed that the GATK would work normally on some part of chromosome, while terminates while...

Alipha-Clisa