#####First downloaded genoscope version of rainbow trout genome as Cornell did

	original file: /workdir/genomes/public/oncorhynchus/mykiss/Oncorhynchus_mykiss_chr.fa.gz
	downloaded http://www.genoscope.cns.fr/trout/data/Oncorhynchus_mykiss_chr.fa.gz on 19 May 2015
	md5sum:49a03c1a76d52450c113237a5fd75a40
	
	chromosomes were renamed in the following manner for compatibility with the GBS pipeline:
	removed leading "chr_", replaced "Un_" with "100", and replaced "Sex" with "999"
	
	using the following commands:
	zcat Oncorhynchus_mykiss_chr.fa.gz | sed 's/chr_//g' | sed 's/chrUn_/100/g' | sed 's/Sex/999/g' | sed
	's/chrUn/100/g' > Oncorhynchus_mykiss_chr.renamed.fa
	
	resulting in the file:
	/workdir/genomes/public/oncorhynchus/mykiss/Oncorhynchus_mykiss_chr.renamed.fa
	of total size (bp) 2170264975
	with md5sum: bdfa882743b5293faa0af9569f00ec2c

#####Used the VCF_2_fasta.py script to convert the VCF file to a fasta file

	kchristensen@ccr:/scratch2/kchristensen/RedWhiteFlesh$ python ./script/VCF_2_Fasta_v1.0.py -vcf ./vcf/all.mergedSNPs.vcf.gz \
	-fasta ./genome/Oncorhynchus_mykiss_chr.renamed.fa -fai ./genome/Oncorhynchus_mykiss_chr.renamed.fa.fai > ./output/all.mergedSNPs.fasta

#####Aligned SNPs to NCBI version of Chinook salmon genome

	kchristensen@ccr:/scratch2/kchristensen/RedWhiteFlesh/output$ blastn -task megablast -outfmt 6 -db ../genome/GCA_002872995.1_Otsh_v1.0_genomic.fna \
	-query ./all.mergedSNPs.fasta -out ./all.mergedSNPs.vs.NCBI.Otsh.ver.1.0.evalue.0.001.mts2.thsps2.aln -evalue 0.001 -max_target_seqs 2 -max_hsps 2 -num_threads 8

#####These alignments were then filtered

	kchristensen@ccr:/scratch2/kchristensen/RedWhiteFlesh$ python ./script/Filter_Alignments_Blast_Fmt6_ver1.0.py -aln_file 
	./output/all.mergedSNPs.vs.NCBI.Otsh.ver.1.0.evalue.0.001.mts2.thsps2.aln -min_per 94 -min_aln 98 -min_dif 2 > \
	./output/all.mergedSNPs.vs.NCBI.Otsh.ver.1.0.evalue.0.001.mts2.thsps2.minper94.minaln98.mindif2.aln


#####The filtered alignments then replaced the old positions in the vcf files (Current values retain roughly half the SNPs in the original vcf file)

	kchristensen@ccr:/scratch2/kchristensen/RedWhiteFlesh$ python ./script/Assign_New_SNP_Possitions.py -aln_file \
	./output/all.mergedSNPs.vs.NCBI.Otsh.ver.1.0.evalue.0.001.mts2.thsps2.minper94.minaln98.mindif2.aln -vcf \
	./vcf/all.mergedSNPs.vcf.gz -gap 2 > ./vcf/all.mergedSNPs.v3.gap2.NCBI.Otsh.V1.vcf

#####The filtered alignments then replaced the old positions in the .map files

	kchristensen@ccr:/scratch2/kchristensen/RedWhiteFlesh$ python ./script/Assign_New_SNP_Possitions.py -aln_file \
	./output/all.mergedSNPs.vs.NCBI.Otsh.ver.1.0.evalue.0.001.mts2.thsps2.minper94.minaln98.mindif2.aln -map \
	./vcf/FilteredGenotypes_GWASpigment_chinook.plk.map -gap 2 > ./vcf/FilteredGenotypes_GWASpigment_chinook.plk.V3.gap2.NCBI.Otsh.V1.0.map