Single Nucleotide Variant Filtering
Individual releases can be downloaded from:
https://github.com/CuppenResearch/SNVFI/releasesAlternatively use git clone:
git@github.com:CuppenResearch/SNVFI.gitSNVFI 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.
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
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> sh SNVFI_run.sh <config> <ini>- GNU/Linux (tested on CentOS Linux release 7.2.1511
- (optional) Sun Grid Engine (tested on SGE 8.1.8)
- 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
- VariantAnnotation
- ggplot2
- reshape2