bwa_dedup

USAGE

bipipe bwa_dedup [--config CONFIG] **params

Example Config File

bwa_dedup.json

{
  "ref_fasta": "/PATH/TO/REFERENCE/genome.fa",
  "bed_file": "/PATH/TO/TARGETS.bed",
  "out_path": "/OUTPUT/DIRECTORY",
  "r1": "/PATH/TO/SAMPLE_R1.fastq.gz",
  "r2": "/PATH/TO/SAMPLE_R2.fastq.gz",
  "sample_name": "SAMPLE_ID",
  "at": "bwtsw",
  "threads": 40,
  "remove_dups": false,
  "remove_seq_dups": false,
  "use_md": false
}

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

bipipe get-config bwa_dedup

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 bwa_dedup_sp_qc_mosdepth pipeline.
--ref_fasta REF_FASTA	No	Path to the reference FASTA file.
--bed_file BED_FILE	No	Path to the BED file for coverage analysis.
--at AT	No	Algorithm type for BWA indexing (default is 'bwtsw').
--out_path OUT_PATH	No	Output directory for results.
--r1 R1	No	Path to the first read FASTQ file.
--r2 R2	No	Path to the second read FASTQ file.
--sample_name SAMPLE_NAME	No	Sample identifier for output files.
--threads THREADS	No	Number of threads to use for processing.
--remove_dups	No	Whether to remove all duplicates (default is False).
--remove_seq_dups	No	Whether to remove sequencing duplicates (default is False).
--use_md	No	Whether to use MarkDuplicatesSpark (default is False).