Plink to VCF

plink --noweb --bfile $plink_file --reference-allele $ref_Allele_file --make-bed --out $plink_file_modified pseq $pseq_project new-project pseq $pseq_project load-plink --file $plink_file_modified --id $plink_file_modified pseq $pseq_project write-vcf | gzip > $plink_file_modified.vcf.gz
 * 1) !/bin/sh
 * 1) 1. have plink/binary to specify reference allele
 * 1) 2. create plinkseq project
 * 1) 3. load plink file into plink/seq
 * 1) 4. write out vcf file