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Converting VCF to BEAGLE format

Can bcftools generate a beagle formatted file from a vcf with genotype likelihoods? If so, how could I do this? I'm not seeing any documentation on this. vcftools has the ability to do so but I want to know if bcftools can do this and how. Thanks!

bcftools variant snp beagle vcf
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written by diversitree • diversitree

1 answer

Try vcftools

--BEAGLE-GL
--BEAGLE-PL

These options output genotype likelihood information for input into the BEAGLE program. The VCF file is required to contain FORMAT fields with "GL" or "PL" tags, which can generally be output by SNP callers such as the GATK. Use of this option requires a chromosome to be specified via the "--chr" option. The resulting output file has the suffix ".BEAGLE.GL" or ".BEAGLE.PL" and contains genotype likelihoods for biallelic sites. This file is suitable for input into BEAGLE via the "like=" argument.

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written by zx8754 zx8754

That would be ideal but I’m running into the problem of having so many contigs (20k +) that I don’t know the best way to specify their names in the --chr flag, which doesn’t accept a list of chromosome names like one per line. Having all 20k names written on the command line or in a script fails because the argument is too long.

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written by diversitree • diversitree

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