I wish to convert a VCF file in the BEAGLE format with all chromosomes contained in the VCF file with vcftools. Unfortunately, it seems there is no option to use vcftools with all the chromosome, at least one chromosome has to be specified in the command.
vcftools --gzvcf GVCF_SNPs.vcf.gz \ --out beagle_file.PL \ --BEAGLE-PL \ --chr chromosome_ID
If the chromosome is omitted, an error message shows up:
Error: Require a chromosome (--chr) when outputting Beagle likelihoods.
Would anyone know why it is the case? Or if there is any way around to process all the chromosomes?