Hi,
To Convert vcf file into .bed, .bim , .fam i used here the following command
java -jar GenomeAnalysisTK.jar -T VariantsToBinaryPed -R chr20_NOPREFIX.fa -V chr20.vcf -m metadata.fam -bed chr20.bed -bim chr20.bim -fam chr20.fam --minGenotypeQuality 0
But is showing the following error:
ERROR MESSAGE: Meta data file not found: /------/-------/metadata.fam
ERROR -----------
So if have to create the .fam file ? how to create this with which command? i am not able to find.