bdolmo / GenePanel-Multimap

Simple perl script to extract mappability from a ROI file

GenePanel-Multimap

Extract mappability scores at every exon entry.

Dependencies

• Perl
• Perl modules: Sort::Key::Natural
• R (>= 3.3). In addition Rscript must be accessible
• ggplot2 R library
• BEDtools
• GEM-mapper

Other required files

• Genome references in FASTA format
• GEM index file

ROI format

ROI file must contain at least four columns (tab-delimited). The 4th column must be formated with this scheme: RefSeq_numericExonPrevious_numericExonCurrent;Gene

Example:

chr17	48243395	48243444	NM_000023_0_1;SGCA
chr17	48244723	48244854	NM_000023_1_2;SGCA

Usage

perl GenePanel-Multimap.pl <Params>

Params:

-bed    FILE   BED file of regions 
-l      INT    Bait length (default 80)
-m      INT    Maximum percentage of mismatches for mapping (default 1%)
-g      FILE   Genome file in FASTA
-ncpu   INT    Number of CPUs used for gem-mapper (default 1)
-index  FILE   PATH to GEM indexed file
-o      FILE   Output directory

Low mappability plots