From VCF to BEAGLE format with multiple chromosomes

Question

[Begonia_pavonina]

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?

[marcela.herrerasarrias]

Hi there,

I'm trying to do exactly the same thing but not working. Did you figure it out?

Thanks!

[Begonia_pavonina]

I have just found a way around with ANGSD, with genotype likelihood in binary glf as an output. But I think you can use the following command to output BEAGLE format files. Here is a link to the documentation: http://www.popgen.dk/angsd/index.php/Genotype_Likelihoods

angsd -GL -doGlf 2

[marcela.herrerasarrias]

Hello,

Yes, but it's not the same thing. I want to use my snp matrix from GATK and not genotype likelihoods from angsd. Did you manage to convert your vcf file to beagle binary using all chromosomes at the same time?

Thanks!

[Begonia_pavonina]

Unfortunately not, I think I have made some trials with PLINK, but didn't follow up on it. Good luck!