CLI Reference

plink2zarr convert

Convert plink fileset to VCF Zarr. Results are equivalent to plink1.9 –bfile prefix –keep-allele-order –recode vcf-iid –out tmp then running vcf2zarr convert tmp.vcf zarr_path

plink2zarr convert [OPTIONS] IN_PATH ZARR_PATH

Options

-f, --force

Force overwriting of existing directories

-p, --worker-processes <worker_processes>

Number of worker processes

Default:

0

-P, --progress, -Q, --no-progress

Show progress bars (default: show)

-v, --verbose

Increase verbosity

-l, --variants-chunk-size <variants_chunk_size>

Chunk size in the variants dimension

-w, --samples-chunk-size <samples_chunk_size>

Chunk size in the samples dimension

Arguments

IN_PATH

Required argument

ZARR_PATH

Required argument