TraFic_filter.pl - Filter clusters
TraFic_filter.pl [-h] -o /some/path/ -r %.out -f %.fa
Required options: --input (-i) Single data file to be filtered NOTE: All files must be formatted to include the first 5 fields as described in Cluster.pm see end of this message. Other options: --filter (-f) One or more files to be used as a filter. --filtmin (-fm) Minimum number of reads required in wt pos/neg cluster data to exclude a cluster. [2] --germ (-g) Pre-calculated Germline events file. --germmin (-gm) Minimum number of reads required in germline cluster data to exclude a cluster. [5] --output (-o) Output written to specified folder as filtered.txt. [.] --tes (-t) Transposable element regions from genome, format mimics clustered file core fields, see below. Exception is TOTAL_READS is replaced with the divergence value. --div (-d) Only user records from -t where divergence is < this value. [200] --readlen (-r) Approximation of read length in input data, as clusters are merged sensible to use max value. [100] --sorted (-s) Assume all inputs are sorted Examples: TraFic_filter -o tumour/filtered/ -i tumour/reciprocal_clusters.txt -f normal/reciprocal_clusters.txt \ -f ref/known_false_pos.txt -f ref/normal_panel.txt \ -t hg19_TEs.txt -d 200
Chromosome or sequence identifier.
Masking identified reads as hitting repeat of this type.
Left most position of cluster.
Left most position of cluster.
Total number of reads that support this cluster