Index Symbols | B | C | E | F | G | H | I | M | N | O | P | R | S | T | V | W Symbols --backend-storage vcztools-index command line option vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --compression-level vcztools-view-bgen command line option --disable-automatic-newline vcztools-query command line option --drop-genotypes vcztools-view command line option --encode-threads vcztools-view command line option --exclude vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --exclude-types vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --fill-tags vcztools-view command line option --fixed-variant-size vcztools-view-bgen command line option --force-samples vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --format vcztools-query command line option --header-only vcztools-view command line option --include vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --list-samples vcztools-query command line option --log-file vcztools-index command line option vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --log-level vcztools-index command line option vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --max-alleles vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --min-alleles vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --no-bgi vcztools-view-bgen command line option --no-bim vcztools-view-plink command line option --no-fam vcztools-view-plink command line option --no-header vcztools-view command line option --no-header-samples vcztools-view-bgen command line option --no-sample-file vcztools-view-bgen command line option --no-update vcztools-view command line option --no-version vcztools-view command line option --nrecords vcztools-index command line option --output vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --pad-byte vcztools-view-bgen command line option --readahead-buffer-size vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --readahead-workers vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --regions vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --regions-file vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --samples vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --samples-file vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --stats vcztools-index command line option --storage-option vcztools-index command line option vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --targets vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --targets-file vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --total-string-length vcztools-view-bgen command line option --types vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option --unphased vcztools-view-bgen command line option --variant-id-field vcztools-view-bgen command line option -e vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -f vcztools-query command line option -G vcztools-view command line option -H vcztools-view command line option -h vcztools-view command line option -I vcztools-view command line option -i vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -l vcztools-query command line option -M vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -m vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -N vcztools-query command line option -n vcztools-index command line option -o vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -R vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -r vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -S vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -s vcztools-index command line option vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -T vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -t vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -V vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option -v vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option B BcftoolsFilter (class in vcztools) bed_size (vcztools.BedEncoder property) BedEncoder (class in vcztools) bgen_size (vcztools.BgenEncoder property) BgenEncoder (class in vcztools) bytes_per_variant (vcztools.FormatEncoder property) C close() (vcztools.FormatEncoder method) contig_ids (vcztools.VczReader property) E evaluate() (vcztools.VariantFilter method) F field_names (vcztools.VczReader property) FieldInfo (class in vcztools) FormatEncoder (class in vcztools) G get_field_info() (vcztools.VczReader method) H header_size (vcztools.BgenEncoder property) I is_fill() (in module vcztools) is_missing() (in module vcztools) M materialise_variant_filter() (vcztools.VczReader method) N num_samples (vcztools.FormatEncoder property) (vcztools.VczReader property) num_variants (vcztools.FormatEncoder property) (vcztools.VczReader property) O open_zarr() (in module vcztools) P pad_byte (vcztools.BgenEncoder property) PATH vcztools-index command line option vcztools-query command line option vcztools-view command line option vcztools-view-bgen command line option vcztools-view-plink command line option prefix_size (vcztools.FormatEncoder property) R raw_sample_ids (vcztools.VczReader property) read() (vcztools.FormatEncoder method) referenced_fields (vcztools.VariantFilter property) S sample_ids (vcztools.VczReader property) scope (vcztools.VariantFilter property) set_sample_indexes() (vcztools.VczReader method) set_samples() (vcztools.VczReader method) set_variant_filter() (vcztools.VczReader method) set_variants() (vcztools.VczReader method) T total_size (vcztools.FormatEncoder property) total_string_length (vcztools.BgenEncoder property) trim_fill() (in module vcztools) try_cached_read() (vcztools.FormatEncoder method) V variant_chunks() (vcztools.VczReader method) variant_id_field (vcztools.BgenEncoder property) variant_offsets (vcztools.BgenEncoder property) VariantFilter (class in vcztools) variants() (vcztools.VczReader method) VczReader (class in vcztools) vcztools-index command line option --backend-storage --log-file --log-level --nrecords --stats --storage-option -n -s PATH vcztools-query command line option --backend-storage --disable-automatic-newline --exclude --force-samples --format --include --list-samples --log-file --log-level --output --readahead-buffer-size --readahead-workers --regions --regions-file --samples --samples-file --storage-option --targets --targets-file -e -f -i -l -N -o -r -R -s -S -t -T PATH vcztools-view command line option --backend-storage --drop-genotypes --encode-threads --exclude --exclude-types --fill-tags --force-samples --header-only --include --log-file --log-level --max-alleles --min-alleles --no-header --no-update --no-version --output --readahead-buffer-size --readahead-workers --regions --regions-file --samples --samples-file --storage-option --targets --targets-file --types -e -G -h -H -I -i -m -M -o -r -R -s -S -t -T -v -V PATH vcztools-view-bgen command line option --backend-storage --compression-level --exclude --exclude-types --fixed-variant-size --force-samples --include --log-file --log-level --max-alleles --min-alleles --no-bgi --no-header-samples --no-sample-file --output --pad-byte --readahead-buffer-size --readahead-workers --regions --regions-file --samples --samples-file --storage-option --targets --targets-file --total-string-length --types --unphased --variant-id-field -e -i -m -M -o -r -R -s -S -t -T -v -V PATH vcztools-view-plink command line option --backend-storage --exclude --exclude-types --force-samples --include --log-file --log-level --max-alleles --min-alleles --no-bim --no-fam --output --readahead-buffer-size --readahead-workers --regions --regions-file --samples --samples-file --storage-option --targets --targets-file --types -e -i -m -M -o -r -R -s -S -t -T -v -V PATH virtual_field_names (vcztools.VczReader property) W write_bgen() (in module vcztools) write_bgi() (in module vcztools) write_bim() (in module vcztools) write_fam() (in module vcztools) write_plink() (in module vcztools) write_sample() (in module vcztools) write_to() (vcztools.FormatEncoder method) write_vcf() (in module vcztools)