Questions tagged [vep]
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VEP annotation INFO field Ensembl IDs and locations
I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line).
However, my output is ...
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How to make a POST "vep/:species/region" request that is able to accomodate multiple alternate alleles for a single variant?
There is an R code example on Ensembl's website on how to execute a POST "vep/:species/region" request for variants that only have one alternate allele. The part that holds the variant data ...
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Different human reference genomes from NCBI and ENSEMBL, and variant annotation with Variant Effect Predictor (VEP)
Background: I have been working on a human variant calling pipeline, from whole exome reads to variant annotation.
For variant annotation I used the Variant Effect predictor (VEP), which is Ensembl ...
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How to calculate the variant allelic fraction (VAF) from VEP output?
This question was also asked on Biostars
How can I calculate the variant allelic fraction from the VEP file for multiple human samples?
I used the ensembl-vep and it is human data.
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How to normalise indel of different transcript direction?
I am trying to reproduce an analysis result, and there is a requirement regarding the format of the result: the '3' rule ': all mutations should be expressed in a position close to the end of the gene ...
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dealing with a list of VEP files
I'm new to dealing with big and compressed data so, I have some questions regarding that
I have 1000 files, each file has the extension (vep.txt.gz) I want to read these files, then filter them. The ...
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Error installing VEP on mac
I have tried multiple different ways to get Ensemble's Variant Effect Predictor (VEP) to properly install on my mac, but I keep getting same error.
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In VEP annotation, how is the codon field interpreted?
After annotating with VEP a VCF file, we obtain different fields. One of them is called Codons which represents the affected codon in the transcript of the gene. ...
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