File explanations:

csv_to_fasta.pl --> turns the input ctgn_snps.csv into a fasta format. 

CTGN_scored_SNPs.txt --> Scored SNPs are created from probe process (Left and right spacing. All are strict. 

ctgn_sequences.fasta --> output of csv_to_fasta.pl. Conversion of ctgn_snps.csv. 

ctgn_snps.csv --> Original input 4,862 probes and their genotypes. 

ctgn.vcf --> pseudo vcf files of CTGN SNPs.

final_formatted_probes_for_alignment.bed --> sam to bed using samtools and bedtools. 

final_formatted_probes_for_alignment.fasta --> Output of reformat_probes_for_alignment.pl. Ready for alignment!

final_formatted_probes_for_alignment.sam --> Output of bowtie2 alignment.

final_formatted_probes_for_alignment_stats.txt --> Samtools alignment statistics.

reformat_probes_for_alignment.pl --> Turns trimmed_selected_probes.txt to final_formatted_probes_for_alignment.fasta. Changes SNP to IUPAC and
	makes format correct for genome alignment using bowtie2.

selection.pl --> Choses from final_formatted_probes_for_alignment.bed those that matched perfectly. 

trimmed_selected_probes.txt --> Trimming ctgn_sequences.fasta to 70 nt segments. 

unannotated_scored_SNPs.txt --> Concat of CTGN_scored_SNPs.txt and scored snps from probe creation without IUPAC sequences.

unannotated_SNP_probes.txt --> Probes created from unannotated_scored_SNPs.txt, but without SNPeff adjustment. 

vcf_from_bed.pl --> Turns selected final_formatted_probes_for_alignment.bed to ctgn.vcf