The time required to load various genotype file formats.
Genotype files must be specified as VCF or BCF files. They can be bgzip-compressed.
There is also experimental support for PLINK2 PGEN files (accomponied by PVAR and PSAM files) in some commands. These files can be loaded and created much more quickly than VCFs, so we highly recommend using them if you're working with large datasets. See the documentation for the :class:`GenotypesPLINK` class in :ref:`the API docs <api-data-genotypesplink>` for more information.
If you run out memory when using PGEN files, consider reading/writing variants from the file in chunks via the --chunk-size parameter.
To convert a VCF containing only biallelic SNPs to PGEN, use the following command.
plink2 --snps-only 'just-acgt' --max-alleles 2 --vcf input.vcf --make-pgen --out outputTo convert a VCF containing tandem repeats to PGEN, use this command, instead.
plink2 --vcf-half-call m --make-pgen 'pvar-cols=vcfheader,qual,filter,info' --vcf input.vcf --make-pgen --out output