gatk_gcnv

USAGE

bipipe gatk_gcnv [--config CONFIG] **params

Example Config File

gatk_gcnv.json

{
  "input_json": "/PATH/TO/INPUT.json",
  "output_dir": "/PATH/TO/OUTPUT_DIR",
  "exome_loc": "/PATH/TO/EXOME_LOC.bed",
  "genome_fasta": "/PATH/TO/REFERENCE/genome.fa",
  "ref_dict": "/PATH/TO/REFERENCE/genome.dict",
  "contig_pp": "/PATH/TO/CONTIG_PLOIDY_PRIORS.tsv",
  "class_coherence_length": "10000",
  "cnv_coherence_length": "10000",
  "min_contig_length": "46709983",
  "p_active": "0.01",
  "p_alt": "0.000001",
  "interval_psi_scale": "0.001"
}

This gatk_gcnv.json can be copied into the current working via

bipipe get-config gatk_gcnv

CLI

Parameters from the configuration file can be overwritten by the command line with the following parameters.

Option	Required	Description
-h, --help	No	Show this help message and exit
--config CONFIG	No	Path to the configuration file for the GATK GCNV pipeline.
--input_json INPUT_JSON	No	Paths to input bams (JSON file)
--output_dir OUTPUT_DIR	No	Path to output directory
--exome_loc EXOME_LOC	No	Path to exome BED file
--genome_fasta GENOME_FASTA	No	Path to genome FASTA file
--ref_dict REF_DICT	No	Path to reference dictionary file
--contig_pp CONTIG_PP	No	Path to contig ploidy prior file
--class_coherence_length CLASS_COHERENCE_LENGTH	No	Class coherence length
--cnv_coherence_length CNV_COHERENCE_LENGTH	No	CNV coherence length
--min_contig_length MIN_CONTIG_LENGTH	No	Minimum contig length
--p_active P_ACTIVE	No	Prior probability of treating an interval as CNV-active
--p_alt P_ALT	No	Total prior probability of alternative copy-number states
--interval_psi_scale INTERVAL_PSI_SCALE	No	Typical scale of interval-specific unexplained variance
--sample_psi_scale SAMPLE_PSI_SCALE	No	Typical scale of sample-specific correction to the unexplained variance