/aminos

Map sequencing variants to proteins at biobank-scale

Primary LanguagePythonMIT LicenseMIT

aminos.png

Overview

Convert large genetic VCF files into FASTA files corresponding to individual's protein sequences. This repo will handle complex combinations of coding variants scaling to biobank-size genetic sequencing datasets.

Install

git clone https://github.com/barneyhill/aminos
cd aminos
pip install -r requirements.txt

Usage

python3 aminos.py --vcf [path-to-vcf] --gff [path-to-gff] --fasta [path-to-fasta] --output [output-directory]

Input Requirements

  1. A GFF3 file containing genomic features. Currently, only Ensembl GFF3 files are supported, see for example ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens.

  2. A VCF file containing phased variant calls. The VCF file should be generated by BCF/csq

  3. A reference fasta file containing transcript ids and the protein sequences of each transcript, for example,

>TRANS_ID
TRANS_SEQ_LINE1
TRANS_SEQ_LINE2 
>TRANS_ID
TRANS_SEQ_LINE1
.
.
.

Output

aminos will write to [output-directory]/[transcript].fa.gz. Within these files will be the variant sequences corresponding to a comma seperated list of associated samples. These samples are formatted {individual_id}_{haplotype}.

Currently supported consequences

  • missense
  • inframe_deletion
  • inframe_insertion

Contact

barney.hill@ndph.ox.ac.uk