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1. Open gene and select platinum data for a trio. Click load and all panels are displayed as expected.
2. Go back to the Data modal.
3. Click 'Single'. The variant and coverage panels for Mother and F…
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Some data sources provide only very broad location information about a sequence alteration (i.e at the level of a chromosome region instead of within a specific gene/marker). @nlwashington can provid…
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Hi,
We are currently using the VEP v111 Docker container to annotate VCF files. However, we are facing the following issues:
1. Performance Issue: Annotation of a very small sample VCF file takes…
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Hi, this is a great idea, and really useful package. 2 quesions:
1. I note from the README.md that this package is "based on the original SAIGE package (v0.29.4.4)". But I'm not certain if that me…
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In `paramlink2`, we need to set the dfreq for diseaseModel.
For example:
`dm = diseaseModel(chrom = "AD", penetrances = c(0,1,1), dfreq = 1e-5)`.
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Was running many samples, all variants with REF allele longer than A, T, C or G were without any interpretation (so all deletions were missing).
What is interesting, with ALT allele longer than one …
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Currently an endpoint for retrieving annotations for an individual case is already exposed in the following endpoint:
https://github.com/bihealth/varfish-server/blob/1e956c92aabfc7fee9caaefaec60f00…
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I am trying to run SAIGE-GWAS Gene and Region Based Association Tests, and I am trying to figure out how to obtain legitimate groupfiles to use for the analysis. I know there is an R-script available,…
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Hi Team - thanks for the great piece of software!
I've hit an issue where prediction is failing on the fasta file from the gene SELENON (attached, changed to .txt to allow upload - [protein.txt](h…
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Hello,
I was wondering if the Gene Filter can be used in command line. I am running oc on a WGS vcf file and my command looks like this:
`oc run file.vcf -l hg19 -a clinvar -t text excel`
The…