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usage: hugeseq [-h] -r FILE [FILE ...] [-R FILE [FILE ...]] [-b] [-s INT] -o
               DIR [-g STR] [-A] [-B] [-C] [-V] [-v TYPE [TYPE ...]] [--itx]
               [--variantonly] [--nobinning] [--nocleanup] [--novariant]
               [-j FILE] [-m SIZE] [-q NAME] [-t COUNT] [--submit]

Generating the job file for the HugeSeq variant detection pipeline

optional arguments:
  -h, --help            show this help message and exit
  -r FILE [FILE ...], --reads1 FILE [FILE ...]
                        The FASTQ file(s) for reads 1
  -R FILE [FILE ...], --reads2 FILE [FILE ...]
                        The FASTQ file(s) for reads 2, if paired-end
  -b, --bam             Support for aligned and coordinate-sorted BAMs as
                        input (-r). No alignment will be performed.
  -s INT, --split INT   Split input into INT reads per file (default: no
  -o DIR, --output DIR  The output directory
  -g STR, --readgroup STR
                        The read group annotation (Default:
  -A, --donealign       Sequences already aligned
  -B, --donebinning     Alignments already binned by chromosomes
  -C, --donecleanup     Alignments already cleaned
  -V, --donevariant     Variants already called
  -v TYPE [TYPE ...], --variants TYPE [TYPE ...]
                        SNP, INDEL, SRA, RPM, RDA, JCT (default to all)
  --ctx                 Transchromosomal rearrangement detection (only
                        relevant in binning mode)
  --variantonly         Only call variants
  --nobinning           Do not bin the alignments by chromosomes
  --nocleanup           Do not clean up the alignments
  --novariant           Do not call variants
  -j FILE, --jobfile FILE
                        The jobfile name (default: stdout)
  -m SIZE, --memory SIZE
                        Memory size (GB) per job (default: 12)
  -q NAME, --queue NAME
                        Queue for jobs (default: extended)
  -t COUNT, --threads COUNT
                        Number of threads for alignment, only works for SGE
                        (default: 1)
  --submit              Submit the jobs