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### Description of the bug
Hi,
This is about the GATK resource bundle but I am opening a bug report here because I encounter this while using this pipeline.
dbSNP138 has the wrong reference alle…
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### Description of feature
**Description**:
I am writing to request the addition of parameters for specifying haploid contigs and regions when detecting SNPs and Indels using DeepVariant in the nf…
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### Description of feature
I often work with non-human germline data and in sarek it is required to specify a patient ID and a sample ID in the samplesheet. The IDs that are then written to the cra…
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**Describe the bug**
Hello
From what I can see, Octopus in tumour-only calling mode sometimes does not detect heterozygous germline variants which have undergone loss of heterozygosity during tumo…
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`cnvkit` output files are missing. There is no segmentation file `.cns` and scatter and diagram plot files `.pdf` in the output folder. They are not generated by `cnvkit batch` module.
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A user on the GATK Forum submitted a request to make the INFO field easier to manipulate through creating a table. At the GATK Office Hours meeting 11/8, we discussed the two ideas and favored the fir…
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Hi,
We want to use CNVkit for CNV calling on somatic data. What kind of VCF file should we use for best results? Should it contain germline or somatic variants or both? Is there any specific caller…
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Hi,
From the `--help` page I've deduced that Sniffles categorizes its parameters in a few categories
- Common parameters
- SV Filtering parameters
- SV Clustering parameters
- Multi-Sample Ca…
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### Description of the bug
Dear All,
I launched the variant calling step using the ASCAT tool, but I received an error message that I did not understand. Could you please help me resolve this issu…
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### Description of the bug
`A USER ERROR has occurred: Bad input: Sample P-*_P-*-REF-100X is not in BAM header: `[*_P-*-REF-100X,*_*-TMN-150X]````
I have the same error as the issue : [https://git…