<<

TraFiC.pl

Reference implementation of Cancer Genome Project transposable element detection.

SYNOPSIS

TraFiC.pl [options]

  Required parameters:
    -outdir    -o   Folder to output result to.
    -tumour    -t   Tumour BAM file
    -normal    -n   Normal BAM file
    -maskdb    -d   RepeatMasker database

  RepeatMasker
    -engine    -e   RepeatMasker engine [ncbi]
    -rm        -r   Path to RepeatMasker binary [search $PATH]
    -tdiv      -td  Tumour max divergence from RepeatMasker database [5]
    -ndiv      -nd  Normal max divergence from RepeatMasker database [10]
    -accuracy  -a   Set the accuracy of RM values map to RM args [0]
                      0 = -s
                      1 = -q
                      2 = -qq

  Clustering
    -support   -s   Minimum supporting reads required to emit a cluster. [5]

  Filtering
    -known     -k   Known genomic events (e.g. TE regions)
    -div       -di  Only user records from -k where divergence is < this value. [200]
    -germline  -g   Pre-calculated germline events (aka Normal Panel)
    -filtmin   -fm  Minimum number of reads required in wt pos/neg cluster data to exclude a cluster. [2]
    -germmin   -gm  Minimum number of reads required in germline cluster data to exclude a cluster. [5]
    -length    -rl  Max read length in input data [100]

  General
    -badloci   -b   bed[.gz] regions to exclude from read selection (e.g. UCSC high depth regions)
    -cpus      -c   Number of cores to use. [1]
                     - recommend max 4 during 'input' process.
    -limit     -l   When defined with '-cpus' internally thread concurrent processes.
                     - requires '-p', specifically for pindel/pin2vcf steps

  Targeted processing (further detail under OPTIONS):
    -process   -p   Only process this step then exit, optionally set -index
    -index     -i   Optionally restrict '-p' to single job
    -jobs      -j  Declare with -p to determine how many jobs are needed for this step

  Other:
    -help      -h   Brief help message.
    -man       -m   Full documentation.
    -version   -v   Version

  File list can be full file names or wildcard, e.g.
    pindel.pl -c 4 -r some/genome.fa[.gz] -o myout -t tumour.bam -n normal.bam

  Run with '-m' for possible input file types.

OPTIONS

-process

Available processes for this tool are:

  select
  split
  mask
  cluster
  filter
-index

Possible index ranges for processes above are:

  select   = 1..2
  split  = 1
  mask = 1..<n>
  cluster   = 1
  filter    = 1

If you want STDOUT/ERR to screen ensure index is set even for single job steps.

<<