Index

Symbols

--column-chunk-size vcf2zarr-dexplode-init command line option vcf2zarr-explode command line option --compressor vcf2zarr-dexplode-init command line option vcf2zarr-explode command line option --contig-id tskit2zarr-convert command line option --force plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option vcf2zarr-encode command line option vcf2zarr-explode command line option zipzarr command line option --isolated-as-ancestral tskit2zarr-convert command line option --isolated-as-missing tskit2zarr-convert command line option --json vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option --keep zipzarr command line option --local-alleles vcf2zarr-convert command line option vcf2zarr-mkschema command line option --max-memory vcf2zarr-encode command line option --max-variant-chunks vcf2zarr-dencode-init command line option vcf2zarr-encode command line option --no-local-alleles vcf2zarr-convert command line option vcf2zarr-mkschema command line option --no-progress plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-finalise command line option vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option vcf2zarr-encode command line option vcf2zarr-explode command line option zipzarr command line option --num-partitions vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option vcfpartition command line option --one-based vcf2zarr-dencode-partition command line option vcf2zarr-dexplode-partition command line option --partition-size vcfpartition command line option --ploidy vcf2zarr-mkschema command line option --progress plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-finalise command line option vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option vcf2zarr-encode command line option vcf2zarr-explode command line option zipzarr command line option --samples-chunk-size plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-init command line option vcf2zarr-encode command line option vcf2zarr-mkschema command line option --schema vcf2zarr-dencode-init command line option vcf2zarr-encode command line option --unzip zipzarr command line option --variants-chunk-size plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-init command line option vcf2zarr-encode command line option vcf2zarr-mkschema command line option --verbose plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-finalise command line option vcf2zarr-dencode-init command line option vcf2zarr-dencode-partition command line option vcf2zarr-dexplode-finalise command line option vcf2zarr-dexplode-init command line option vcf2zarr-dexplode-partition command line option vcf2zarr-encode command line option vcf2zarr-explode command line option vcf2zarr-inspect command line option vcfpartition command line option zipzarr command line option --version vcfpartition command line option zipzarr command line option

--worker-processes plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dexplode-init command line option vcf2zarr-encode command line option vcf2zarr-explode command line option --zarr-format plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-init command line option vcf2zarr-encode command line option -C vcf2zarr-dexplode-init command line option vcf2zarr-explode command line option -c vcf2zarr-dexplode-init command line option vcf2zarr-explode command line option -f plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option vcf2zarr-encode command line option vcf2zarr-explode command line option zipzarr command line option -k zipzarr command line option -l plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-init command line option vcf2zarr-encode command line option vcf2zarr-mkschema command line option -M vcf2zarr-encode command line option -n vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option vcfpartition command line option -P plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-finalise command line option vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option vcf2zarr-encode command line option vcf2zarr-explode command line option zipzarr command line option -p plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dexplode-init command line option vcf2zarr-encode command line option vcf2zarr-explode command line option -Q plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-finalise command line option vcf2zarr-dencode-init command line option vcf2zarr-dexplode-init command line option vcf2zarr-encode command line option vcf2zarr-explode command line option zipzarr command line option -s vcf2zarr-dencode-init command line option vcf2zarr-encode command line option vcfpartition command line option -u zipzarr command line option -V vcf2zarr-dencode-init command line option vcf2zarr-encode command line option -v plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-finalise command line option vcf2zarr-dencode-init command line option vcf2zarr-dencode-partition command line option vcf2zarr-dexplode-finalise command line option vcf2zarr-dexplode-init command line option vcf2zarr-dexplode-partition command line option vcf2zarr-encode command line option vcf2zarr-explode command line option vcf2zarr-inspect command line option vcfpartition command line option zipzarr command line option -w plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-init command line option vcf2zarr-encode command line option vcf2zarr-mkschema command line option

C

convert() (in module bio2zarr.plink) (in module bio2zarr.tskit) (in module bio2zarr.vcf)

D

DEST zipzarr command line option

I

ICF_PATH vcf2zarr-dencode-init command line option vcf2zarr-dexplode-finalise command line option vcf2zarr-dexplode-init command line option vcf2zarr-dexplode-partition command line option vcf2zarr-encode command line option vcf2zarr-explode command line option vcf2zarr-mkschema command line option

IN_PATH plink2zarr-convert command line option

P

PARTITION vcf2zarr-dencode-partition command line option vcf2zarr-dexplode-partition command line option PATH vcf2zarr-inspect command line option plink2zarr-convert command line option --force --no-progress --progress --samples-chunk-size --variants-chunk-size --verbose --worker-processes --zarr-format -f -l -p -P -Q -v -w IN_PATH ZARR_PATH

S

SRC zipzarr command line option

T

TS_PATH tskit2zarr-convert command line option tskit2zarr-convert command line option --contig-id --force --isolated-as-ancestral --isolated-as-missing --no-progress --progress --samples-chunk-size --variants-chunk-size --verbose --worker-processes --zarr-format -f -l -P -p -Q -v -w TS_PATH ZARR_PATH

V

vcf2zarr-convert command line option --force --local-alleles --no-local-alleles --no-progress --progress --samples-chunk-size --variants-chunk-size --verbose --worker-processes --zarr-format -f -l -P -p -Q -v -w VCFS ZARR_PATH vcf2zarr-dencode-finalise command line option --no-progress --progress --verbose -P -Q -v ZARR_PATH vcf2zarr-dencode-init command line option --force --json --max-variant-chunks --no-progress --num-partitions --progress --samples-chunk-size --schema --variants-chunk-size --verbose --zarr-format -f -l -n -P -Q -s -V -v -w ICF_PATH ZARR_PATH vcf2zarr-dencode-partition command line option --one-based --verbose -v PARTITION ZARR_PATH vcf2zarr-dexplode-finalise command line option --verbose -v ICF_PATH vcf2zarr-dexplode-init command line option --column-chunk-size --compressor --force --json --no-progress --num-partitions --progress --verbose --worker-processes -c -C -f -n -P -p -Q -v ICF_PATH VCFS

vcf2zarr-dexplode-partition command line option --one-based --verbose -v ICF_PATH PARTITION vcf2zarr-encode command line option --force --max-memory --max-variant-chunks --no-progress --progress --samples-chunk-size --schema --variants-chunk-size --verbose --worker-processes --zarr-format -f -l -M -P -p -Q -s -v -V -w ICF_PATH ZARR_PATH vcf2zarr-explode command line option --column-chunk-size --compressor --force --no-progress --progress --verbose --worker-processes -c -C -f -P -p -Q -v ICF_PATH VCFS vcf2zarr-inspect command line option --verbose -v PATH vcf2zarr-mkschema command line option --local-alleles --no-local-alleles --ploidy --samples-chunk-size --variants-chunk-size -l -w ICF_PATH vcfpartition command line option --num-partitions --partition-size --verbose --version -n -s -v VCFS VCFS vcf2zarr-convert command line option vcf2zarr-dexplode-init command line option vcf2zarr-explode command line option vcfpartition command line option

Z

ZARR_PATH plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-dencode-finalise command line option vcf2zarr-dencode-init command line option vcf2zarr-dencode-partition command line option vcf2zarr-encode command line option zipzarr command line option --force --keep --no-progress --progress --unzip --verbose --version -f -k -P -Q -u -v DEST SRC