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I am running GATK GenotypeGVCFs, v4.2.6.1. I am trying to call Genotypes on a GenomicsDB workspace with about 500 WGS samples. Note, this is the macaque MMul10 genome, so it has 2,939 contigs (includi…
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Hi,
I am using the latest version and cache for VEP (v.100) on GRCh37 and noticed that when using --SYMBOL option, some of the gene names in the SYMBOL column are outdated one. I learned from anoth…
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Hi Pete!
Today I'll be going through a few variants that my validation script ran into, so you might get a few issues reported by me today.
I'm not sure if these are useful, but I have a few exa…
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Hi dear Ensembl team,
I'm having some issues because I would like to annotate my genetic variants based on the canonical isoforms from UniProt, but I can't find a way to do it. Sometimes the MANE …
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Hello!
I was attempting to try out the biovalidator but I am running into errors and not sure where I am going wrong. Thanks in advance for any help or advice you can offer!
The inputs I am usin…
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### What container were you trying to use, and how were you attempting to use it?
[dongyibo@login8 variants]$ singularity exec -B ./:/data docker://staphb/snpeff:5.1 snpEff ann Candida_auris /blue/bp…
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Hi Sam,
Thanks for the great tutorial. I have been trying PLINK for the polygenic risk score. However, with the height dataset and EUR plink files, I am not able to reproduce the results. Especially,…
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### Project short name:
RiskVariantsAF
### Primary Wrangler:
Ida
### Secondary Wrangler:
Anu
### Associated files
* Google Drive: [folder](https://drive.google.com/drive/folders/1n7c2XL4e6KUKqum2few…
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An initial quick hack seems to imply that CRAM support might be quite easy to add. The only difficult bit is probably ensuring that the required references are present, and telling htslib where to fin…
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Initial thoughts and proposals outline below, based on info collected in the requirements doc [here](https://docs.google.com/document/d/1J4AqGDEqyK8KAzfiowgHYKJNvzHuwHSHgkN9dleLemY/edit#heading=h.b3a9…