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Hi,
I'm trying to use the COCOS plugin with vep (version 95) and it doesn't seem to be producing the cocos.fasta file that is expected when successful. No vep errors or relevant warnings appeared …
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Hi @morungos,
So VEP has run successfully on the COSMIC v75 CosmicCodingMuts.vcf file via `perl cosmic.pl --force`
This took around 28 hours on my little laptop, finishing with ~3.3 million varian…
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I have already been using Adam with snpEff annotations and it worked great. However, when I've tried to use it with a VCF file annotated using Ensembl VEP it didn't work. I was expecting, that ANN for…
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One of the differences between VEP and varcode is that VEP is happy to annotate ALL transcripts in its database, including pseudo-genes. Varcode will limit itself to transcripts which have [`Transcrip…
joaoe updated
8 years ago
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> We're specifically hoping to sort by the consequence on the amino acid chain (e.g. p.Trp417Ter is a nonsense variant, c.1225-1G>T is a splicing variant, and p.Lys464SerfsTer24 is a frameshift varian…
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#### Feature Description
In #7294, we automated upgrading and downgrading the build version by 1 major version. There are some additional scenarios that should be tested to ensure that we are complyi…
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Hi Daniel
i am running Loftee and getting these two error.
1. Use of uninitialized value in string eq at /home/ubuntu/.vep/Plugins/LoF.pm line 309.
2. WARNING: Failed to instantiate plugin LoF…
Melb1 updated
3 years ago
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**Snakemake version**
Snakemake: 5.19.2
Conda: 4.8.3
Singularity: 3.5.3
Those are installed by `conda create -n pvacseq_msi python=3.7 snakemake=5.19.2 pandas=1.0.1 singularity=3.5.3`
**Descr…
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Genmod version: 3.7.0 (replicated in 3.7.2 as well)
command: `genmod score -s --skip_plugin_check -f sample.ped -c rank_model.ini -t ped new_sample.vcf `
I am using a custom made rank model with…
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dbSNP is missing for this variant (https://www.genomenexus.org/variant/17:g.41276045_41276046del) due to missing data on myvariantinfo (https://www.genomenexus.org/variant/17:g.41276045_41276046del). …
jjgao updated
3 years ago