snv_indel

USAGE

bipipe snv_indel [--config CONFIG] **params

Example Config File

snv_indel.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",
  "scatter_count": 48,
  "germline_resource": "/PATH/TO/GERMLINE_RESOURCE.vcf.gz",
  "index_image": "/PATH/TO/INDEX_IMAGE.img",
  "downsampling_stride": null,
  "panel_of_normals": null,
  "variants_for_contamination": null,
  "max_reads_per_alignment_start": null,
  "max_suspicious_reads_per_alignment_start": null,
  "max_population_af": null,
  "lrom": true,
  "interval_padding": 100,
  "tumor_samples": [
    {
      "sample_id": "TUMOR_SAMPLE_ID",
      "r1": "/PATH/TO/TUMOR_R1.fastq.gz",
      "r2": "/PATH/TO/TUMOR_R2.fastq.gz"
    },
    {
      "sample_id": "TUMOR_SAMPLE_ID1",
      "r1": "/PATH/TO/TUMOR_R1.fastq.gz",
      "r2": "/PATH/TO/TUMOR_R2.fastq.gz"
    },
    {
      "sample_id": "TUMOR_SAMPLE_ID2",
      "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"
    },
    {
      "sample_id": "NORMAL_SAMPLE_ID1",
      "r1": "/PATH/TO/NORMAL_R1.fastq.gz",
      "r2": "/PATH/TO/NORMAL_R2.fastq.gz"
    },
    {
      "sample_id": "NORMAL_SAMPLE_ID2",
      "r1": "/PATH/TO/NORMAL_R1.fastq.gz",
      "r2": "/PATH/TO/NORMAL_R2.fastq.gz"
    }
  ]
}

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

bipipe get-config snv_indel

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 SNV/Indel 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.
--scatter_count SCATTER_COUNT	No	Scatter count.
--germline_resource GERMLINE_RESOURCE	No	Path to the germline resource VCF.
--index_image INDEX_IMAGE	No	Path to the index image.
--downsampling_stride DOWNSAMPLING_STRIDE	No	Downsampling stride.
--panel_of_normals PANEL_OF_NORMALS	No	Panel of normals file.
--variants_for_contamination VARIANTS_FOR_CONTAMINATION	No	Variants for contamination file.
--max_reads_per_alignment_start MAX_READS_PER_ALIGNMENT_START	No	Max reads per alignment start.
--max_suspicious_reads_per_alignment_start MAX_SUSPICIOUS_READS_PER_ALIGNMENT_START	No	Max suspicious reads per alignment start.
--max_population_af MAX_POPULATION_AF	No	Max population allele frequency.
--lrom	No	Enable LROM.
--interval_padding INTERVAL_PADDING	No	Interval padding.
--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.