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## Bug Report
### Affected tool(s) or class(es)
Mutect2
### Affected version(s)
4.4.0.0
### Description
Hello GATK team,
I am working on a pipeline that calls variants using Mutect2 an…
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### Installation Type
Docker
### pVACtools Version / Docker Image
Docker container, version 4.4.1
### Python Version
_No response_
### Operating System
_No response_
### Descri…
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Ubuntu 18.04
htslib 1.15.1-19-g3c44c0b
"liftover" at 1.21-25-g9d314180
80 cpu
512GB RAM
I am attempting to liftover a VCF of ~5 million variants for a single sample. I have tried a BCF, and ind…
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Hi,
I am working on annotating large datasets, specifically Whole Genome Sequencing (WGS) VCF files, using the Variant Effect Predictor (VEP). However, the annotation process is taking significantl…
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I don't know if here is the right place to ask this, probably not. If someone knows where is the right place please tell me.
I'm using VCFFileReader to read the file and then
`CloseableIterator vc = …
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### Description of the bug
gnomAD SV v4.1 (https://gnomad.broadinstitute.org/news/2023-11-v4-structural-variants/) contains some CNVs that don't have AC or AF information in the vcf (gnomad.v4.1.sv.s…
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### Description of the bug
Hi there
Thank you for the pipeline, it was working good using just frebayes. now add sarek and mutec.
I need to find structural mutations, and de novo mutation, however …
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The rule annotate_vep does not run before annotate_esm.
After the checkpoint prescore, the snakemake pipeline directly runs annotate_esm.
It says that inside the snakefile, the input of annota…
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Hi,
A great tool for reads simulation, and I am trying to use it on my data.
`seqToProfile` requires an VCF file as an input file. But the configuration file for `simuReads` requires (option…
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If the VCF has "CLNSIG=Likely_pathogenic;", it will incorrectly match the _Pathogenic_-rule (which has higher priority than the _Likely pathogenic_-rule, since "Pathogenic" is a substring of "Likely_p…