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Rosemeis / pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
GNU General Public License v3.0
46 stars 11 forks source link

Support for VCF input #59

Open fgvieira opened 2 years ago

fgvieira commented 2 years ago

Dear all,

are there any plans to support VCF input? It would be nice if it would support genotypes, and both the GL and PL likelihoods.

Not sure if it might help, but with bcftools it is possible to convert a VCF to "almost" a beagle format:

bcftools query --format "%CHROM\t%POS\t%REF\t%ALT[\t%GL]\n"

Maybe this format would be easier to read internally? thanks,