Uses GATK, Picard, and BEDTools to:
1.) Make a FASTA subset for regions of interest with corresponding .dict and .fai files
2.) Identify positions of N-strings above a user-specified threshold (returns coordinates for ACGTmers and Nmers)
3.) Convert .interval_list file to .bed file
4.) Merge regions into windows of an approximate (user-specified) size
5.) Format for use in pipeline as a .bed file
Uses GATK, Picard, and BEDTools to: 1.) Make a FASTA subset for regions of interest with corresponding .dict and .fai files 2.) Identify positions of N-strings above a user-specified threshold (returns coordinates for ACGTmers and Nmers) 3.) Convert .interval_list file to .bed file 4.) Merge regions into windows of an approximate (user-specified) size 5.) Format for use in pipeline as a .bed file