Index

Symbols

--biowulf cgr-submit command line option --bpm-file <bpm_file> cgr-config command line option --ccad2 cgr-submit command line option --cgems cgr-config command line option cgr-submit command line option --cgems-dev cgr-config command line option --cluster-group-size <cluster_group_size> cgr-pre-flight command line option --cluster-profile <cluster_profile> cgr-submit command line option --config-file <config_file> cgr-pre-flight command line option --dry-run cgr-submit command line option --genome-build <genome_build> cgr-config command line option --include-unused-settings cgr-config command line option --local-mem-mb <local_mem_mb> cgr-submit command line option --local-tasks <local_tasks> cgr-submit command line option --max-threads <max_threads> cgr-submit command line option --no-biowulf cgr-submit command line option --no-ccad2 cgr-submit command line option --no-cgems cgr-submit command line option --no-dry-run cgr-submit command line option

--no-notemp cgr-submit command line option --no-reference-files-check cgr-pre-flight command line option --no-slurm cgr-submit command line option --no-update-config cgr-pre-flight command line option --no-user-files-check cgr-pre-flight command line option --notemp cgr-submit command line option --project-name <project_name> cgr-config command line option --queue <queue> cgr-submit command line option --sample-sheet <sample_sheet> cgr-config command line option --slurm cgr-submit command line option --slurm-partition <slurm_partition> cgr-config command line option --submission-cmd <submission_cmd> cgr-submit command line option --subworkflow <subworkflow> cgr-submit command line option --threads <threads> cgr-pre-flight command line option --time-hr <time_hr> cgr-submit command line option -j cgr-pre-flight command line option -s cgr-config command line option -u cgr-config command line option -y cgr-config command line option

A

address_a (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute) address_b (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute) addresses (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute)

AdpcBase (class in cgr_gwas_qc.parsers.illumina.adpc) AdpcReader (class in cgr_gwas_qc.parsers.illumina.adpc) AdpcWriter (class in cgr_gwas_qc.parsers.illumina.adpc) assay_type (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute)

B

BeadPoolManifest (class in cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) BimFile (class in cgr_gwas_qc.parsers.bim)

BimRecord (class in cgr_gwas_qc.parsers.bim) BpmFile (class in cgr_gwas_qc.parsers.bpm) BpmRecord (class in cgr_gwas_qc.parsers.bpm)

C

cgr-config command line option --bpm-file <bpm_file> --cgems --cgems-dev --genome-build <genome_build> --include-unused-settings --project-name <project_name> --sample-sheet <sample_sheet> --slurm-partition <slurm_partition> -s -u -y cgr-pre-flight command line option --cluster-group-size <cluster_group_size> --config-file <config_file> --no-reference-files-check --no-update-config --no-user-files-check --threads <threads> -j cgr-submit command line option --biowulf --ccad2 --cgems --cluster-profile <cluster_profile> --dry-run --local-mem-mb <local_mem_mb> --local-tasks <local_tasks> --max-threads <max_threads> --no-biowulf --no-ccad2 --no-cgems --no-dry-run --no-notemp --no-slurm --notemp --queue <queue> --slurm --submission-cmd <submission_cmd> --subworkflow <subworkflow> --time-hr <time_hr>

cgr_gwas_qc.parsers.bim module cgr_gwas_qc.parsers.bpm module cgr_gwas_qc.parsers.eigensoft module cgr_gwas_qc.parsers.graf module cgr_gwas_qc.parsers.illumina.adpc module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles module cgr_gwas_qc.parsers.king module cgr_gwas_qc.parsers.plink module cgr_gwas_qc.workflow.scripts.agg_population_qc_tables module cgr_gwas_qc.workflow.scripts.sample_qc_table module cgr_gwas_qc.workflow.scripts.snp_qc_table module chrom (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute) chroms (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute) complement() (in module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) components (cgr_gwas_qc.parsers.eigensoft.Eigenvec attribute) control_config (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute)

E

Eigenvec (class in cgr_gwas_qc.parsers.eigensoft)

F

FakeData (class in cgr_gwas_qc.testing.data)

filename (cgr_gwas_qc.parsers.eigensoft.Eigenvec attribute)

G

GenotypeCalls (class in cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) get_autocall_date() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_autocall_version() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_ballele_freqs() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_base_calls() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_base_calls_forward_strand() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_base_calls_generic() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_base_calls_plus_strand() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_call_rate() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_cluster_file() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_control_x_intensities() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_control_y_intensities() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_gc10() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_gc50() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_gender() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_genotype_scores() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_genotypes() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_imaging_date() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_logr_dev() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method)

get_logr_ratios() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_normalization_transforms() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_normalized_intensities() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_num_calls() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_num_intensity_only() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_num_no_calls() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_num_snps() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_percentiles_x() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_percentiles_y() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_ploidy() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_ploidy_type() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_raw_x_intensities() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_raw_y_intensities() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_record_problems() (cgr_gwas_qc.parsers.bim.BimRecord method) get_sample_name() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_sample_plate() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_sample_well() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_scanner_data() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_slide_identifier() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method) get_snp_manifest() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method)

I

is_write_complete() (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls method)

L

LocusEntry (class in cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles)

M

manifest_name (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute) map_info (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute) module cgr_gwas_qc.parsers.bim cgr_gwas_qc.parsers.bpm cgr_gwas_qc.parsers.eigensoft cgr_gwas_qc.parsers.graf cgr_gwas_qc.parsers.illumina.adpc cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles cgr_gwas_qc.parsers.king cgr_gwas_qc.parsers.plink cgr_gwas_qc.workflow.scripts.agg_population_qc_tables cgr_gwas_qc.workflow.scripts.sample_qc_table cgr_gwas_qc.workflow.scripts.snp_qc_table

N

name (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute)

normalization_lookups (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute) num_loci (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute)

O

open() (in module cgr_gwas_qc.parsers.bim) (in module cgr_gwas_qc.parsers.bpm)

R

read_byte() (in module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) read_char() (in module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) read_float() (in module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) read_genome() (in module cgr_gwas_qc.parsers.plink) read_het() (in module cgr_gwas_qc.parsers.plink) read_hwe() (in module cgr_gwas_qc.parsers.plink) read_imiss() (in module cgr_gwas_qc.parsers.plink) read_int() (in module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) read_lmiss() (in module cgr_gwas_qc.parsers.plink)

read_related() (in module cgr_gwas_qc.parsers.king) read_relatedness() (in module cgr_gwas_qc.parsers.graf) read_scanner_data() (in module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) read_sexcheck() (in module cgr_gwas_qc.parsers.plink) read_string() (in module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) read_ushort() (in module cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles) RealData (class in cgr_gwas_qc.testing.data) ref_strand (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute) ref_strands (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute)

S

snp (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute) snps (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute)

source_strand (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.LocusEntry attribute) source_strands (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.BeadPoolManifest attribute) supported_versions (cgr_gwas_qc.parsers.illumina.IlluminaBeadArrayFiles.GenotypeCalls attribute)

V

values (cgr_gwas_qc.parsers.eigensoft.Eigenvec attribute)

W

write() (cgr_gwas_qc.parsers.bpm.BpmFile method)