Many NGS variant analysis tasks require generation of variants in variant call format (VCF). These files are large and inconsistently formatted. This package allows one to run basic snpEff annotation on a variant call format VCF file and then convert this output to a wide table. One can use the output to load into a database system for quick lookup and filtering on different column names.
The input VCF files must be compressed and indexed with tabix. To prepare raw VCF files that are not compressed or tabix-indexed, do:
#Make input files tabix compressed
bgzip file.vcf
tabix -p vcf file.vcf.gz
A UNIX/Linux environment is ideal for running this pipeline. I've been running this on Mac OSX and Ubuntu OS. This is a command line program.
Clone/Download this repository and optionally add the folder location to your UNIX ${PATH}.
- snpEff (>= version 4)
- tabix ( version 0.2.5 or higher).
- bcftools (Version: 1.3 (using htslib 1.3) or higher)
- R (> 3.1.2)
- R data.table i.e.
- R stringr
installation of R packages can be done as following
install.packages(c("stringr","data.table"))
Once you have a snpEff database e.g. hg19, Set the $SNPEFF variable in the vcf_shortAnnotationTable.sh script to the snpEff installation on your system. A minimum memory requirement of ~2G RAM is recommended to run this pipeline.
.Run the pipeline as below
vcf_shortAnnotationTable.sh snpeff_db input.vcf.gz output
If you're simply trying to convert an annotated VCF file without wanting to run snpEff then you may do the following
VCF_printAllTags.sh inputvariants.vcf.gz > output.tsv
Each INFO field in the VCF will be printed.
To parse out these fields in a very quick and dirty way, one can do
The VCFAnno package is a great toolset to use
bash vcfToTable/VCF_printAllTags.sh inputvariants.anno.vcf.gz |perl -w vcfToTable/effParser.pl > output.txt 2> warnings.txt