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Indel analysis script to calculate impact scores (alt/ref ratios). Reference TFBS threshold is 85%. 

Run perl -i <VCF-file> -b <BED-file> -m <matrix file> -o <output file>

BED-file is a BED-formatted file with the list of TFBSs to look for indels within. 

Matrix file can contain PFMs or PWMs. 

Have an "allScoresDir" in the directory you run the script from (or just modify to create the directory in the script). 

Compile littleprogram_indels.cpp before running the program.