Convert VCF to Hapmap

Directions

• First step

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

gatk VariantsToTable \
-V test.vcf \
-R Genome.fa \
-F CHROM -F POS -F REF -F ALT -GF GT \
-O output.table   

Note: you need to specify INPUT_VCF, and OUTPUT.table.

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.

• Second step

 	Rscript convert-vcf-to-hapmap.R -i output.table -o vcf_converted_to_hapmap.txt

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