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1 answer
48 views

Variants from multiple tools: normalization before or after annotation with VEP?

We want to compare some variant calling tools and their calls on Whole Exome Sequencing data. We will have to normalize the variants that are called (.vcf format) before comparison using for instance ...
2 votes
0 answers
25 views

Trouble Running VEP in Conda Environment Due to Perl DBD::mysql Error

Hello StackExchange Community, I am currently facing issues with running the Variant Effect Predictor (VEP) and vcf2maf in a Conda environment due to a Perl-related error. Installation Steps: I ...
0 votes
1 answer
67 views

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 ...
1 vote
0 answers
29 views

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 ...
3 votes
0 answers
74 views

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 ...
0 votes
1 answer
139 views

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.
3 votes
0 answers
36 views

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 ...
3 votes
2 answers
295 views

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 ...
5 votes
2 answers
489 views

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. ...
2 votes
0 answers
55 views

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. ...