VCFextractor is a unix based software that requires no prerequisites to run. This script will take any VCF file and output functional information from the file itself, or from the ExAC rest api database http://exac.hms.harvard.edu
Download VCFextractor.sh
chmod 750 VCFextractor.sh.
export PATH=$PATH:/PATH/TO/VCFextractorDIRECTORY
To run VCFextractor simply call the following command in the terminal
COMMAND == VCFextractor.sh PATH/TO/FILE.vcf [OPTIONS] [OUTPUT]
If not options are included, all options will be outputted
The order of the options placed in command will represent the output order
--INFO == Output from VCF chromosome(#CHROM), position(POS), reference allele(REF) and alternative allele(ALT)
--Variant_Type == Output from VCF TYPE Variant Type(Variant_Type)
--Total_Read_Depth == Output from VCF DP Total Read Depth(Total_Read_Depth)
--Variant_Read_Depth == Output from VCF AO Variant Read Depth(Variant_Read_Depth)
--Reference_Read_Depth == Output from VCF RO Reference Read Depth(Reference_Read_Depth)
--Percentage_Variant_Reads == Output from VCF AO/(AO+RO)x100 Percentage Variant Reads(Percentage_Variant_Reads)
--Variant_Allele_Frequency == Output from VCF AF Variant Allele Frequency(Variant_Allele_Frequency)
--ExAC_ALL == Output from ExAC Browser Variant Consequence(ExAC_ordered_csqs), Allele Frequency(ExAC_allele_freq), RSID(ExAC_rsid)
--ExAC_ordered_csqs == Output from ExAC Browser Variant Orderred Consequence(ExAC_ordered_csqs)
--ExAC_allele_freq == Output from ExAC Browser Variant Allele Frequency(ExAC_allele_freq)
--ExAC_rsid == Output from ExAC Browser Variant RSID(ExAC_rsid)
-tsv == Tab separated file (default)
-csv == Comma separated file
VCFextractor.sh coding_challenge_final.vcf
VCFextractor.sh coding_challenge_final.vcf --Variant_Type --ExAC_ordered_csqs --Total_Read_Depth --Variant_Read_Depth --Percentage_Variant_Reads --Variant_Allele_Frequency --ExAC_allele_freq --ExAC_rsid --INFO --Reference_Read_Depth -csv