cnv

USAGE

bipipe cnv [--config CONFIG] **params

Example Config File

cnv.json

{
  "algotype": "bwtsw",
  "index_fasta": false,
  "aligner_threads": 40,
  "remove_all_duplicates": true,
  "remove_sequencing_duplicates": false,
  "use_gatk_mark_duplicates": true,
  "use_dragen": false,
  "output_folder": "/PATH/TO/OUTPUT/FOLDER",
  "run_name": "RUN_NAME",
  "ref_fasta": "/PATH/TO/REFERENCE/genome.fa",
  "ref_dict": "/PATH/TO/REFERENCE/genome.dict",
  "interval_list": "/PATH/TO/INTERVAL_LIST.interval_list",
  "common_sites": "/PATH/TO/COMMON_SITES.interval_list",
  "pon": "/PATH/TO/PON.pon.hdf5",
  "blacklist_intervals": "/PATH/TO/BLACKLIST.interval_list",
  "minimum_base_quality": 30,
  "number_of_eigensamples": null,
  "minimum_total_allele_count_case": null,
  "minimum_total_allele_count_normal": null,
  "genotyping_homozygous_log_ratio_threshold": null,
  "genotyping_base_error_rate": null,
  "maximum_number_of_segments_per_chromosome": null,
  "kernel_variance_copy_ratio": null,
  "kernel_variance_allele_fraction": null,
  "kernel_scaling_allele_fraction": null,
  "kernel_approximation_dimension": null,
  "window_size": [8,16,32,64,128,256],
  "number_of_changepoints_penalty_factor": null,
  "minor_allele_fraction_prior_alpha": null,
  "number_of_samples_copy_ratio": null,
  "number_of_burn_in_samples_copy_ratio": null,
  "number_of_samples_allele_fraction": null,
  "number_of_burn_in_samples_allele_fraction": null,
  "smoothing_credible_interval_threshold_copy_ratio": null,
  "smoothing_credible_interval_threshold_allele_fraction": null,
  "maximum_number_of_smoothing_iterations": null,
  "number_of_smoothing_iterations_per_fit": null,
  "neutral_segment_copy_ratio_lower_bound": null,
  "neutral_segment_copy_ratio_upper_bound": null,
  "outlier_neutral_segment_copy_ratio_z_score_threshold": null,
  "calling_copy_ratio_z_score_threshold": null,
  "minimum_contig_length": null,
  "maximum_copy_ratio": null,
  "point_size_copy_ratio": null,
  "point_size_allele_fraction": null,
  "tumor_samples": [
    {
      "sample_id": "TUMOR_SAMPLE_ID",
      "r1": "/PATH/TO/TUMOR_R1.fastq.gz",
      "r2": "/PATH/TO/TUMOR_R2.fastq.gz"
    }
  ],
  "normal_samples": [
    {
      "sample_id": "NORMAL_SAMPLE_ID",
      "r1": "/PATH/TO/NORMAL_R1.fastq.gz",
      "r2": "/PATH/TO/NORMAL_R2.fastq.gz"
    }
  ]
}

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

bipipe get-config cnv

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 CNV pipeline.
--algotype ALGOTYPE	No	Algorithm type for BWA indexing.
--index_fasta	No	Whether to index the FASTA file.
--aligner_threads ALIGNER_THREADS	No	Number of threads for the aligner.
--remove_all_duplicates	No	Remove all duplicates.
--remove_sequencing_duplicates	No	Remove sequencing duplicates.
--use_gatk_mark_duplicates	No	Use GATK MarkDuplicates.
--use_dragen	No	Use DRAGEN.
--output_folder OUTPUT_FOLDER	No	Output folder for results.
--run_name RUN_NAME	No	Run name.
--ref_fasta REF_FASTA	No	Path to the reference FASTA file.
--ref_dict REF_DICT	No	Path to the reference dictionary file.
--interval_list INTERVAL_LIST	No	Path to the interval list file.
--common_sites COMMON_SITES	No	Path to the common sites interval list.
--pon PON	No	Panel of normals HDF5 file.
--blacklist_intervals BLACKLIST_INTERVALS	No	Path to blacklist intervals file.
--minimum_base_quality MINIMUM_BASE_QUALITY	No	Minimum base quality.
--number_of_eigensamples NUMBER_OF_EIGENSAMPLES	No	Number of eigensamples.
--minimum_total_allele_count_case MINIMUM_TOTAL_ALLELE_COUNT_CASE	No	Minimum total allele count (case).
--minimum_total_allele_count_normal MINIMUM_TOTAL_ALLELE_COUNT_NORMAL	No	Minimum total allele count (normal).
--genotyping_homozygous_log_ratio_threshold GENOTYPING_HOMOZYGOUS_LOG_RATIO_THRESHOLD	No	Genotyping homozygous log ratio threshold.
--genotyping_base_error_rate GENOTYPING_BASE_ERROR_RATE	No	Genotyping base error rate.
--maximum_number_of_segments_per_chromosome MAXIMUM_NUMBER_OF_SEGMENTS_PER_CHROMOSOME	No	Max segments per chromosome.
--kernel_variance_copy_ratio KERNEL_VARIANCE_COPY_RATIO	No	Kernel variance copy ratio.
--kernel_variance_allele_fraction KERNEL_VARIANCE_ALLELE_FRACTION	No	Kernel variance allele fraction.
--kernel_scaling_allele_fraction KERNEL_SCALING_ALLELE_FRACTION	No	Kernel scaling allele fraction.
--kernel_approximation_dimension KERNEL_APPROXIMATION_DIMENSION	No	Kernel approximation dimension.
--window_size WINDOW_SIZE [WINDOW_SIZE ...]	No	Window sizes.
--number_of_changepoints_penalty_factor NUMBER_OF_CHANGEPOINTS_PENALTY_FACTOR	No	Changepoints penalty factor.
--minor_allele_fraction_prior_alpha MINOR_ALLELE_FRACTION_PRIOR_ALPHA	No	Minor allele fraction prior alpha.
--number_of_samples_copy_ratio NUMBER_OF_SAMPLES_COPY_RATIO	No	Number of samples (copy ratio).
--number_of_burn_in_samples_copy_ratio NUMBER_OF_BURN_IN_SAMPLES_COPY_RATIO	No	Burn-in samples (copy ratio).
--number_of_samples_allele_fraction NUMBER_OF_SAMPLES_ALLELE_FRACTION	No	Number of samples (allele fraction).
--number_of_burn_in_samples_allele_fraction NUMBER_OF_BURN_IN_SAMPLES_ALLELE_FRACTION	No	Burn-in samples (allele fraction).
--smoothing_credible_interval_threshold_copy_ratio SMOOTHING_CREDIBLE_INTERVAL_THRESHOLD_COPY_RATIO	No	Smoothing credible interval threshold (copy ratio).
--smoothing_credible_interval_threshold_allele_fraction SMOOTHING_CREDIBLE_INTERVAL_THRESHOLD_ALLELE_FRACTION	No	Smoothing credible interval threshold (allele fraction).
--maximum_number_of_smoothing_iterations MAXIMUM_NUMBER_OF_SMOOTHING_ITERATIONS	No	Max smoothing iterations.
--number_of_smoothing_iterations_per_fit NUMBER_OF_SMOOTHING_ITERATIONS_PER_FIT	No	Smoothing iterations per fit.
--neutral_segment_copy_ratio_lower_bound NEUTRAL_SEGMENT_COPY_RATIO_LOWER_BOUND	No	Neutral segment copy ratio lower bound.
--neutral_segment_copy_ratio_upper_bound NEUTRAL_SEGMENT_COPY_RATIO_UPPER_BOUND	No	Neutral segment copy ratio upper bound.
--outlier_neutral_segment_copy_ratio_z_score_threshold OUTLIER_NEUTRAL_SEGMENT_COPY_RATIO_Z_SCORE_THRESHOLD	No	Outlier neutral segment copy ratio z-score threshold.
--calling_copy_ratio_z_score_threshold CALLING_COPY_RATIO_Z_SCORE_THRESHOLD	No	Calling copy ratio z-score threshold.
--minimum_contig_length MINIMUM_CONTIG_LENGTH	No	Minimum contig length.
--maximum_copy_ratio MAXIMUM_COPY_RATIO	No	Maximum copy ratio.
--point_size_copy_ratio POINT_SIZE_COPY_RATIO	No	Point size (copy ratio).
--point_size_allele_fraction POINT_SIZE_ALLELE_FRACTION	No	Point size (allele fraction).
--tumor_samples TUMOR_SAMPLES	No	JSON string or path to tumor samples list.
--normal_samples NORMAL_SAMPLES	No	JSON string or path to normal samples list.