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NAME

TraFic_filter.pl - Filter clusters

SYNOPSIS

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

Input format

CHR

Chromosome or sequence identifier.

FAMILY

Masking identified reads as hitting repeat of this type.

L_POS

Left most position of cluster.

R_POS

Left most position of cluster.

TOTAL_READS

Total number of reads that support this cluster

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