I have a set of HLA typed casr/control variant files annotated and with a single tab delimited file for each individual.
#Chromo Position Reference Change Change_type 5 32548555 C A SNP Hom 4 32548561 C G SNP Hom
I wonder whether I can create a PED file with these files. I thought of creating a BED file and then trying to convert it to PED. But since not all the variants are present in each of the individuals, I'm not sure of a way to automate the creation of PED since the variant genotypes should be in exactly same order for all the individuals. One approach would be to take all the annotated tab files and create a single VCF with sample names and convert it to a PED. Yet im not sure how to do that. Even a smallest clues is highly appreciated. Thanks in advance :)