# File explantaions:

35bp_probe_stats.pl and  SNPeff_table.txt --> Can produce SNPeff based statistics. Needs table as second argument. 

	Run as:	perl probe_stats.pl [probes] SNPeff_table.txt > out_stats.txt

70_mer_probes_from_adjusted_scores.pl --> creates probes from adjusted scored_SNPs file. Input arguments are in the script. 

annotated_scored_SNPs.txt  --> Scored SNPs with SNPeff info attached.

final_PITA_probe_stats.txt --> Statistics on final probes created by 35bp_probe_stats.pl

final_PITA_probes.txt --> Final 194,397 probe set

inform_SNPs_with_kmer_table.pl --> A script that uses the kmer hit table to mark high mapping SNPs as HIGHMAP. Creates annotated_scored_SNPs.txt.

MQ_probe_filter.pl --> Filters probes for length, flanking SNPs, and flanking indels. 
	Rules:
		1. No STRICT flanking SNPs anywhere in the sequence
		2. STANDARD flanking SNPs can only be in outer 20nt of probes
		3. Probe must be full length
		4. No indels anywhere in flanking sequence

MQ_probes.txt	--> output of MQ_probe_filter.pl

scored_SNPs_mapping_adjusted.txt --> SNP scores with HIGHMAP SNPS marked.

scored_SNPs.txt --> Output of 70_mer_probes_from_adjusted_scores.pl

SNP_probes.txt --> unfiltered output of 70_mer_probes_from_adjusted_scores.pl.