Hello, I want to output genotype likelihood BEAGLE file from VCF file with angsd, in order to use them in pcangsd later. But with the following command I obtain an error message.

angsd \
    -GL 2 \
        -out output_file \
        -nThreads 10 \
        -doGlf 2 \
        -doMajorMinor 1 \
        -SNP_pval 1e-6 \
        -doMaf 1 \
    -vcf-pl VCF_file.vcf.gz \
    -fai reference_genome.fasta.fai \
    -nInd 159


Can't calculate genotype likelihoods from -glf/-glf3/VCF files

I know the standard method is to use BAM files as input in angsd, but my VCF have been filtrated, and are better input than raw BAM files. Have you found a way to use angsd with VCF files?