SNVFI

Single Nucleotide Variant Filtering

New features present in this fork

• Filter on MQ
• Select chromosomes you want to analyze
• Possibility to remove indels
• Filter on maximum number of alleles per site

Download

Individual releases can be downloaded from:

    https://github.com/ToolsVanBox/SNVFI

Alternatively use git clone:

    git@github.com:ToolsVanBox/SNVFI

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>
    MQ=<Minimum MQ quality>
    CHR="1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X" 		#Specifiy chromosomes with spaces
    CHR_NAM=<Name for the chosen selection of chromosomes. For example 'autosomal'>
    SNV_only=<YES | NO>
    max_alleles=<Maximum number of alleles that can be present at a given site>

    MAIL=<Mail address for qsub>

    CLEANUP=<YES|NO>

Run SNVFI

    sh SNVFI_run.sh <config> <ini>

The full path needs to be given for both the config and ini file.

Dependencies

OS

- GNU/Linux (tested on CentOS Linux release 7.6.1810)

Grid Engine

- (optional) Sun Grid Engine (tested on SGE 8.1.9)

Standalone tools

- R 3.5.0 (https://www.r-project.org)
- bio-vcf 0.9.2 (https://rubygems.org/gems/bio-vcf/versions/0.9.2)
- htslib 1.8 (http://www.htslib.org)
- vcftools 0.1.15 (https://vcftools.github.io)
- zgrep, grep 3.1

R libraries

- VariantAnnotation 1.26.1
- ggplot2 3.0.0
- reshape2 1.4.3