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Using the example code to convert HGVS to VCF, when I put in a HGVS transcript with a duplication, the output for the ref and alt is incorrect. I have tested this with other HGVS nomenclature and thi…
Mchhu updated
11 months ago
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### TMB calculation today in BALSAMIC
The current definition is based on https://github.com/Clinical-Genomics/BALSAMIC/issues/51
And the related snakemake rule https://github.com/Clinical-Genomics…
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_Note: Specific regions were substituted by ``, `` and `` to hide sensitive information. Real usage did not contain brackets._
After combining region of interest locations with `bedtools` to build …
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### Installation Type
Standalone
### pVACtools Version / Docker Image
3.1.1
### Python Version
_No response_
### Operating System
_No response_
### Describe the bug
hello,
With ref-transcrip…
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Dear Peter and guys:
1. I think these days most GWAS don’t have REF and ALT that “must match reference genome” (required by pheweb). Also, I think in the long run, this idea of “REF” allele in t…
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Hi! It's me again! I finally have the variant call against the genome of one of the parents. If I understood well I need to add a parameter --parent parent_genome.fasta, right? Then my question is, do…
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Hi,
I have 9 diseases/disorders I would like to request a MONDO ID for based on gene curations performed using the ClinGen framework
[Mondo_bulk_submission_ILMN_17_Nov_2023.xlsx](https://github.com…
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The [DNA/substitution page](https://hgvs-nomenclature.org/stable/recommendations/DNA/substitution/) lists the following question and answer:
> "How can I shorten the descriptions of SNPs in a manus…
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Hi Shujun,
Thanks as always for EDTA!
I think this is a silly question - I'm having trouble figuring out how to specify the paths for the genomes I'm putting into panEDTA so the existing annotat…
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## Need
Background to this feature can be found here: https://github.com/Clinical-Genomics/BALSAMIC/issues/1166
In short the need is to remove this filter `--exclude 'FORMAT/AF[0] > 1.0' --soft-…