Index

Symbols

--column-chunk-size vcf2zarr-dexplode-init command line option vcf2zarr-explode command line option --compression-level bgen2zarr-convert command line option --compressor bgen2zarr-convert command line option vcf2zarr-dexplode-init command line option vcf2zarr-explode command line option --contig-id tskit2zarr-convert command line option --dimension-source bgen2zarr-convert command line option --dosage bgen2zarr-convert command line option --float-dtype bgen2zarr-convert command line option --force bgen2zarr-convert command line option 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-ploidy bgen2zarr-convert command line option --max-variant-chunks vcf2zarr-dencode-init command line option vcf2zarr-encode command line option --no-dosage bgen2zarr-convert command line option --no-local-alleles vcf2zarr-convert command line option vcf2zarr-mkschema command line option --no-probabilities bgen2zarr-convert command line option --no-progress bgen2zarr-convert command line option 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-convert command line option vcf2zarr-mkschema command line option --probabilities bgen2zarr-convert command line option --probability-model bgen2zarr-convert command line option --progress bgen2zarr-convert command line option 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 --sample-file bgen2zarr-convert command line option --sample-id-column bgen2zarr-convert command line option --sample-ids bgen2zarr-convert command line option --samples-chunk-size bgen2zarr-convert command line option 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 bgen2zarr-convert command line option 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 bgen2zarr-convert command line option plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-create-index 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 bgen2zarr-convert command line option 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 bgen2zarr-convert command line option 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 bgen2zarr-convert command line option 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 bgen2zarr-convert command line option 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 bgen2zarr-convert command line option 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 bgen2zarr-convert command line option 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 bgen2zarr-convert command line option 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 bgen2zarr-convert command line option plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-create-index 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 bgen2zarr-convert command line option 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

B

bgen2zarr-convert command line option --compression-level --compressor --dimension-source --dosage --float-dtype --force --max-ploidy --no-dosage --no-probabilities --no-progress --probabilities --probability-model --progress --sample-file --sample-id-column --sample-ids --samples-chunk-size --variants-chunk-size --verbose --worker-processes --zarr-format -f -l -p -P -Q -v -w BGEN_PATH ZARR_PATH

BGEN_PATH bgen2zarr-convert command line option

C

convert() (in module bio2zarr.bgen) (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 --ploidy --progress --samples-chunk-size --variants-chunk-size --verbose --worker-processes --zarr-format -f -l -P -p -Q -v -w VCFS ZARR_PATH vcf2zarr-create-index command line option --verbose -v 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 bgen2zarr-convert command line option plink2zarr-convert command line option tskit2zarr-convert command line option vcf2zarr-convert command line option vcf2zarr-create-index 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