Entering edit mode
13 months ago
Begonia_pavonina
▴
150
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?