SNVFI

Single Nucleotide Variant Filtering

Download

Individual releases can be downloaded from:

    https://github.com/CuppenResearch/SNVFI/releases

Alternatively use git clone:

    git@github.com:CuppenResearch/SNVFI.git

Usage

SNVFI is configured using a config file, and an ini file for each filtering run. In most scenarios you'll create the config file once and create an ini file per filtering run.

Edit SVNFI_default.config

    SNVFI_ROOT=<path to SNFVI install directory>
    BIOVCF_PREFIX=<path to bio-vcf executable>
    TABIX_PREFIX=<path to tabix executable>
    VCFTOOLS_PREFIX=<path to vcftools executable>
    R_PREFIX=<path to R executable>
    RSCRIPT=<path to SNVFI_filtering_R.R R-script>
    MAX_THREADS=<maximum number of threads used by SNFVI>
    SGE=<YES|NO> #Use Sun Grid Engine yes or no

Edit SNVFI_dummy.ini

    SNV=<Path to input vcf>
    SUB=<Subject column in vcf>
    CON=<Control column in vcf>
    OUT_DIR=<Output directory>

    BLACKLIST=(
    '<blacklist1.vcf>'
    '<blacklist2.vcf>'
    );

    SUB_GQ=<Minimum Genotype Quality in subject sample>
    CON_GQ=<Minimum Genotype Quality in control sample>
    QUAL=<Minimum quality threshold>
    COV=<Minimum coverage threshold>
    FILTER=<Select either ALL variants or only PASS>
    VAF=<Variant Allele Frequency threshold>
    

    MAIL=<Mail address for qsub>

    CLEANUP=<YES|NO>

Run SNVFI

    sh SNVFI_run.sh <config> <ini>

Dependencies

OS

- GNU/Linux (tested on CentOS Linux release 7.2.1511

Grid Engine

- (optional) Sun Grid Engine (tested on SGE 8.1.8)

Standalone tools

- R >= 3.2.2 (https://www.r-project.org)
- bio-vcf 0.9.2 (https://rubygems.org/gems/bio-vcf/versions/0.9.2)
- tabix 0.2.6 (http://www.htslib.org)
- vcftools 0.1.14 (https://vcftools.github.io)
- zgrep, grep

R libraries

- VariantAnnotation
- ggplot2
- reshape2