tushardave26 / simvar

Simulate Variants for provided genomic coordinates

SimVar [alpha version]

Simulate Variants for provided genomic coordinates

Description

SimVar - a tool that can simulate the variants for a given genomic location/s.

Pre-requisites

• Python 3.6 or greater version [Add python3.6 link here]

Dependencies

Required Pyhton3.6 modules

• click-7.0
• pysam-0.15.2

Input

• BED file with all the genomic coordinates of interest
• Reference Genome file in FASTA format
• Reference Genome Index file (i.e. fai)

Output

Variant file in CSV format containing the following columns:

• chr - chromosome name
• start - Start position
• end - End position
• ref - Reference allele
• alt - Alternate allele

Usage

$ ./simvar.py --help
Usage: simvar.py [OPTIONS]

  Simple program that generate the universe of variants for given genomic
  location.

Options:
  -o, --out PATH      an ouptput file name [default: STDOUT]
  -i, --ref-idx PATH  Index file for reference genome  [required]
  -r, --ref PATH      Reference genome file in FASTA format  [required]
  -b, --bed PATH      BED file containing the genomic location  [required]
  --help              Show this message and exit.

License

Copyright © 2019-2021 Tushar Dave