gorliver/convert-vcf-to-hapmap

Convert VCF to Hapmap

Directions

Use the GATK tool, VariantsToTable, to first select only genotype information from the vcf file.

	java -Xmx8g -jar GenomeAnalysisTK.jar \
     	-R REFERENCE_GENOME.fa \
     	-T VariantsToTable \
    	 -V INPUT_VCF.vcf \
    	 -F CHROM -F POS -F ID -F QUAL -F REF -F ALT -F QUAL -F FILTER -F INFO -F FORMAT \
    	 -o OUTPUT.txt \
    	 -AMD \
    	 -GF GT 

Note: you need to specify REFERENCE_GENOME.fa, INPUT_VCF, and OUTPUT.vcf.

Then use the R script called from the command line to convert the variant table to hapmap. Note, this is only tested for haploid, biallelic SNP data.

 	Rscript --vanilla vcf2hapmap.R OUTPUT.vcf HAPMAP.txt

OUTPUT.txt is the output table from the VariantsToTable tool, and HAPMAP.txt is the output file name.

You may need to change the first line of the vcf2hapmap.r script depending on where R is installed.