Reference implementation of Cancer Genome Project transposable element detection.
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.
Available processes for this tool are:
select split mask cluster filter
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.