Copy
aligner
ANTIBODY_bc_bases_with_q30_frac
ANTIBODY_bc_bases_with_q30_in_gel_bead_frac
ANTIBODY_bc_bases_with_q30_in_probe_frac
ANTIBODY_chemistry
ANTIBODY_feature_reads_in_cells
ANTIBODY_filtered_bcs_transcriptome_union
ANTIBODY_frac_feature_reads_usable
ANTIBODY_good_bc_frac
ANTIBODY_good_bc_in_gel_bead_frac
ANTIBODY_good_bc_in_probe_frac
ANTIBODY_good_umi_frac
ANTIBODY_multi_cdna_pcr_dupe_reads_frac
ANTIBODY_multi_filtered_bcs
ANTIBODY_multi_filtered_bcs_median_counts
ANTIBODY_multi_usable_reads_per_filtered_bc
ANTIBODY_read_bases_with_q30_frac
ANTIBODY_reads_lost_to_aggregate_GEMs
ANTIBODY_reads_per_cell
ANTIBODY_recognized_feature_bc_frac
ANTIBODY_recognized_feature_bc_frac_in_filtered_barcodes
ANTIBODY_total_read_pairs
ANTIBODY_total_read_pairs_in_filtered_barcodes
ANTIBODY_umi_bases_with_q30_frac
ANTIBODY_unprocessed_read_pairs
ANTIGEN_bc_bases_with_q30_frac
ANTIGEN_bc_bases_with_q30_in_gel_bead_frac
ANTIGEN_bc_bases_with_q30_in_probe_frac
ANTIGEN_chemistry
ANTIGEN_feature_reads_in_cells
ANTIGEN_good_bc_frac
ANTIGEN_good_umi_frac
ANTIGEN_multi_cdna_pcr_dupe_reads_frac
ANTIGEN_multi_filtered_bcs
ANTIGEN_multi_filtered_bcs_median_counts
ANTIGEN_multi_usable_reads_per_filtered_bc
ANTIGEN_read_bases_with_q30_frac
ANTIGEN_reads_per_cell
ANTIGEN_total_read_pairs
ANTIGEN_total_read_pairs_in_filtered_barcodes
ANTIGEN_umi_bases_with_q30_frac
ANTIGEN_unprocessed_read_pairs
avx
bc_bases_with_q30_frac
bc_bases_with_q30_in_gel_bead_frac
bc_bases_with_q30_in_probe_frac
bin_filesystem
cgroup_memory_hard_limit
cgroup_memory_soft_limit
chain
check_library_compatibility
chemistry
chemistry_name
container
core_hours
cores_per_socket
cpu_mfg
create_bam
CRISPR_bc_bases_with_q30_frac
CRISPR_bc_bases_with_q30_in_gel_bead_frac
CRISPR_bc_bases_with_q30_in_probe_frac
CRISPR_chemistry
CRISPR_feature_bc_extracted_frac
CRISPR_feature_bc_extracted_frac_in_filtered_barcodes
CRISPR_feature_reads_in_cells
CRISPR_frac_cells_with_multiple_protospacer
CRISPR_frac_cells_with_protospacer
CRISPR_frac_feature_reads_usable
CRISPR_good_bc_frac
CRISPR_good_bc_in_gel_bead_frac
CRISPR_good_bc_in_probe_frac
CRISPR_good_umi_frac
CRISPR_multi_cdna_pcr_dupe_reads_frac
CRISPR_multi_filtered_bcs
CRISPR_multi_filtered_bcs_median_counts
CRISPR_multi_usable_reads_per_filtered_bc
CRISPR_read_bases_with_q30_frac
CRISPR_reads_per_cell
CRISPR_recognized_feature_bc_frac
CRISPR_recognized_feature_bc_frac_in_filtered_barcodes
CRISPR_total_read_pairs
CRISPR_total_read_pairs_in_filtered_barcodes
CRISPR_umi_bases_with_q30_frac
CRISPR_unprocessed_read_pairs
CRISPR_unrecognized_feature_bc_frac
CRISPR_unrecognized_feature_bc_frac_in_filtered_barcodes
Custom_bc_bases_with_q30_frac
Custom_bc_bases_with_q30_in_gel_bead_frac
Custom_bc_bases_with_q30_in_probe_frac
Custom_chemistry
Custom_feature_reads_in_cells
Custom_good_bc_frac
Custom_good_umi_frac
Custom_multi_cdna_pcr_dupe_reads_frac
Custom_multi_filtered_bcs
Custom_multi_filtered_bcs_median_counts
Custom_multi_usable_reads_per_filtered_bc
Custom_read_bases_with_q30_frac
Custom_reads_per_cell
Custom_total_read_pairs
Custom_total_read_pairs_in_filtered_barcodes
Custom_umi_bases_with_q30_frac
Custom_unprocessed_read_pairs
denovo
disk_hwm
distro
emptydrops_minimum_umis
enable-tsne
error
estimated_gdna_content
estimated_gdna_unspliced_threshold
event_count
expect_cells
failed_stage
feature_r1_length
feature_r2_length
filter_aggregates
filtered_bcs_transcriptome_union
filtered_reads_per_filtered_bc
filter_high_occupancy_gems
filter_probes
force_cells
gene_expression_r1_length
gene_expression_r2_length
GEX_chemistry
glibc
global_minimum_umis
good_bc_frac
good_umi_frac
IGH_vdj_assembly_prod_cdr_bc_frac
IGH_vdj_assembly_umis_per_cell_median
IGH_vdj_recombinome_mapped_reads_frac
IGK_IGH_vdj_assembly_contig_pair_productive_full_len_bc_frac
IGK_vdj_assembly_prod_cdr_bc_frac
IGK_vdj_assembly_umis_per_cell_median
IGK_vdj_recombinome_mapped_reads_frac
IGL_IGH_vdj_assembly_contig_pair_productive_full_len_bc_frac
IGL_vdj_assembly_prod_cdr_bc_frac
IGL_vdj_assembly_umis_per_cell_median
IGL_vdj_recombinome_mapped_reads_frac
include_introns
jobmode
kernel
median_genes_per_singlet
median_umi_per_singlet
memgb
memory
min_assignment_confidence
min_contig_length
min_crispr_umi
min-crispr-umi
multi_cdna_pcr_dupe_reads_frac
multi_filtered_bcs_conf_mapped_barcoded_reads_cum_frac
multiplet_filter
MULTIPLEXING_bc_bases_with_q30_frac
MULTIPLEXING_bc_bases_with_q30_in_gel_bead_frac
MULTIPLEXING_bc_bases_with_q30_in_probe_frac
MULTIPLEXING_chemistry
MULTIPLEXING_feature_reads_in_cells
MULTIPLEXING_good_bc_frac
MULTIPLEXING_good_umi_frac
MULTIPLEXING_multi_cdna_pcr_dupe_reads_frac
MULTIPLEXING_read_bases_with_q30_frac
MULTIPLEXING_reads_per_cell
MULTIPLEXING_total_read_pairs
MULTIPLEXING_umi_bases_with_q30_frac
MULTIPLEXING_unprocessed_read_pairs
multi_raw_vdj_paired_clonotype_diversity
multi_transcriptome_conf_mapped_reads_frac_in_filtered_barcodes
multi_transcriptome_half_mapped_reads_frac_in_filtered_barcodes
multi_transcriptome_mapped_reads_frac_in_filtered_barcodes
multi_transcriptome_split_mapped_reads_frac_in_filtered_barcodes
multi_transcriptome_targeted_conf_mapped_reads_frac_in_filtered_barcodes
multi_vdj_assembly_contig_pair_productive_full_len_bc_count
multi_vdj_assembly_contig_pair_productive_full_len_bc_frac
multi_vdj_recombinome_mapped_reads_frac
no_bam
no_libraries
normalize
nosecondary
nthreads
pipestance_filesystem
processor_count
process_ulimit
r1_length
r2_length
read_bases_with_q30_frac
reads_per_cell
runtime
shared_contig_filter
singlets_assigned_to_other_samples
singlets_assigned_to_this_sample
skip_cell_annotation
skip_clonotyping
socket_count
subcommand
total_cell_associated_partitions
total_genes_detected
total_read_pairs
total_read_pairs_in_filtered_barcodes
total_singlets
transparent_huge_pages
TRA_TRB_vdj_assembly_contig_pair_productive_full_len_bc_frac
TRA_vdj_assembly_prod_cdr_bc_frac
TRA_vdj_assembly_umis_per_cell_median
TRA_vdj_recombinome_mapped_reads_frac
TRB_vdj_assembly_prod_cdr_bc_frac
TRB_vdj_assembly_umis_per_cell_median
TRB_vdj_recombinome_mapped_reads_frac
TRD_vdj_assembly_prod_cdr_bc_frac
TRD_vdj_assembly_umis_per_cell_median
TRG_TRD_vdj_assembly_contig_pair_productive_full_len_bc_frac
TRG_vdj_assembly_prod_cdr_bc_frac
TRG_vdj_assembly_umis_per_cell_median
umi_baseline_filter
umi_bases_with_q30_frac
unprocessed_read_pairs
utime
vdj_assemblable_read_pairs_per_filtered_bc
VDJ_bc_bases_with_q30_frac
VDJ_B_chemistry
VDJ_chemistry
vdj_filtered_bcs
vdj_filtered_bcs_cum_frac
vdj_good_bc_frac
VDJ_read_bases_with_q30_frac
VDJ_T_chemistry
VDJ_T_GD_chemistry
vdj_total_raw_read_pairs_per_filtered_bc
VDJ_total_read_pairs
VDJ_umi_bases_with_q30_frac
VDJ_unprocessed_read_pairs
vmem_ulimit