cnv_pon

USAGE

bipipe cnv_pon [--config CONFIG] **params

Example Config File

cnv_pon.json

{
  "output_folder": "/PATH/TO/OUTPUT/FOLDER",
  "ref_fasta": "/PATH/TO/REFERENCE/genome.fa",
  "ref_dict": "/PATH/TO/REFERENCE/genome.dict",
  "interval_list": "/PATH/TO/INTERVAL_LIST.interval_list",
  "pon_id": "PON_ID",
  "normal_bams": [
    "/PATH/TO/NORMAL1.bam",
    "/PATH/TO/NORMAL2.bam",
    "/PATH/TO/NORMAL3.bam"
  ],
  "gc_correction": true,
  "bin_length": 10000,
  "blacklist_intervals": "/PATH/TO/BLACKLIST.interval_list",
  "padding": 250,
  "do_impute_zeros": true,
  "number_of_eigensamples": 20,
  "feature_query_lookahead": 1000000,
  "minimum_interval_median_percentile": 10.0,
  "maximum_zeros_in_sample_percentage": 5.0,
  "maximum_zeros_in_interval_percentage": 5.0,
  "extreme_sample_median_percentile": 2.5,
  "extreme_outlier_truncation_percentile": 0.1,
  "maximum_chunk_size": 16777216

}

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

bipipe get-config cnv_pon

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 PON pipeline.
--output_folder OUTPUT_FOLDER	No	Output folder for results.
--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.
--pon_id PON_ID	No	Panel of Normals ID.
--normal_bams NORMAL_BAMS [NORMAL_BAMS ...]	No	List of normal BAM files.
--gc_correction	No	Enable GC correction.
--bin_length BIN_LENGTH	No	Bin length.
--blacklist_intervals BLACKLIST_INTERVALS	No	Path to blacklist intervals file.
--padding PADDING	No	Padding value.
--do_impute_zeros	No	Impute zeros.
--number_of_eigensamples NUMBER_OF_EIGENSAMPLES	No	Number of eigensamples.
--feature_query_lookahead FEATURE_QUERY_LOOKAHEAD	No	Feature query lookahead.
--minimum_interval_median_percentile MINIMUM_INTERVAL_MEDIAN_PERCENTILE	No	Minimum interval median percentile.
--maximum_zeros_in_sample_percentage MAXIMUM_ZEROS_IN_SAMPLE_PERCENTAGE	No	Maximum zeros in sample percentage.
--maximum_zeros_in_interval_percentage MAXIMUM_ZEROS_IN_INTERVAL_PERCENTAGE	No	Maximum zeros in interval percentage.
--extreme_sample_median_percentile EXTREME_SAMPLE_MEDIAN_PERCENTILE	No	Extreme sample median percentile.
--extreme_outlier_truncation_percentile EXTREME_OUTLIER_TRUNCATION_PERCENTILE	No	Extreme outlier truncation percentile.
--maximum_chunk_size MAXIMUM_CHUNK_SIZE	No	Maximum chunk size.