# SIngle population run.
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=1 --rules="1-Inf=1" --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_1OPA --mayobest --minscore=0.4 --default_score=-99
# Run with identical functional class (intron) for all tag SNPs
perl RunSNPPicker2.pl --ps=Kullo4paper_identical_func.csv --pop=CEU --pop=AFR --nOPA=1 --rules="1-Inf=1" --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_1OPA_samefunc --mayobest --minscore=0.4 --default_score=-99
# Run with identical score (0.85)for all tag SNPs with score >=0.4
perl RunSNPPicker2.pl --ps=Kullo4paper_identical_score.csv --pop=CEU --pop=AFR --nOPA=1 --rules="1-Inf=1" --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_1OPA_samescore --mayobest --minscore=0.4 --default_score=-99


perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=2 --rules="1-Inf=1" --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_2OPA --mayobest --minscore=0.4 --default_score=-99
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=3 --rules="1-Inf=1" --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_3OPA --mayobest --minscore=0.4 --default_score=-99
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_1OPA/kullo_ceu_afr_one_snp_1OPA" --minscore=0.4 --nOPA=1 --report_suffix=".out" > kullo_ceu_afr_one_snp_1OPA.soln_log
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_2OPA/kullo_ceu_afr_one_snp_2OPA" --minscore=0.4 --nOPA=2 --report_suffix=".out" > kullo_ceu_afr_one_snp_2OPA.soln_log
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_3OPA/kullo_ceu_afr_one_snp_3OPA" --minscore=0.4 --nOPA=2 --report_suffix=".out" > kullo_ceu_afr_one_snp_3OPA.soln_log
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=1   --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_1OPA_defrules --mayobest --minscore=0.4 --default_score=-99
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=2   --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_2OPA_defrules --mayobest --minscore=0.4 --default_score=-99
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=3   --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_3OPA_defrules --mayobest --minscore=0.4 --default_score=-99
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_1OPA_defrules/kullo_ceu_afr_one_snp_1OPA_defrules" --minscore=0.4 --nOPA=1 --report_suffix=".out" > kullo_ceu_afr_one_snp_1OPA_defrules.soln_log
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_2OPA_defrules/kullo_ceu_afr_one_snp_2OPA_defrules" --minscore=0.4 --nOPA=2 --report_suffix=".out" > kullo_ceu_afr_one_snp_2OPA_defrules.soln_log
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_3OPA_defrules/kullo_ceu_afr_one_snp_3OPA_defrules" --minscore=0.4 --nOPA=3 --report_suffix=".out" > kullo_ceu_afr_one_snp_3OPA_defrules.soln_log
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=1   --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_1OPA_defrules_p098 --mayobest --minscore=0.4 --default_score=-99 --minprob=0.98
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=2   --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_2OPA_defrules_p098 --mayobest --minscore=0.4 --default_score=-99 --minprob=0.98
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=3   --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_one_snp_3OPA_defrules_p098 --mayobest --minscore=0.4 --default_score=-99 --minprob=0.98
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_1OPA_defrules_p098/kullo_ceu_afr_one_snp_1OPA_defrules_p098" --minscore=0.4 --nOPA=1 --report_suffix=".out" > kullo_ceu_afr_one_snp_1OPA_defrules_p098.soln_log
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_2OPA_defrules_p098/kullo_ceu_afr_one_snp_2OPA_defrules_p098" --minscore=0.4 --nOPA=2 --report_suffix=".out" > kullo_ceu_afr_one_snp_2OPA_defrules_p098.soln_log
perl TagSolutionReport.pl --report_prefix="kullo_ceu_afr_one_snp_3OPA_defrules_p098/kullo_ceu_afr_one_snp_3OPA_defrules_p098" --minscore=0.4 --nOPA=3 --report_suffix=".out" > kullo_ceu_afr_one_snp_3OPA_defrules_p098.soln_log

perl RunMultipop.pl --reportname=multipop_ceu_afr_one_snp_1OPA  --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir=SNPApp_AFR_0.90_0.05_1228_1232 --pop=CEU --pop=AFR --mayobest --usescore --usecontext --minscore=0.4 --default_score=-99   > multipop_ceu_afr_one_snp_1OPA.log

java -jar SNPPicker.jar -p CEU -p AFR -im  multipop_ceu_afr_one_snp_1OPA_all.txt  -s Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv  -nOPA -1 -computeutilityonly -r "1-Inf=1" -o multipop_ceu_afr_one_snp_1OPA_all_SNPPicker.txt -minscore 0.4 -e multipop_ceu_afr_one_snp_1OPA_all_SNPPicker.err -defaultscore -99 > log_multi_ceu_afr_snppicker
perl TagSolutionReport.pl --allinonefile=multipop_ceu_afr_one_snp_1OPA_all_SNPPicker.txt --minscore=0.4 --nOPA=-1 > multipop_ceu_afr_one_snp_-1OPA_all_SNPPicker.soln_log
#Unix ((java -jar SNPPicker.jar -p CEU -p AFR -im  multipop_ceu_afr_one_snp_1OPA_all.txt  -s Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv  -nOPA -1 -computeutilityonly -r "1-Inf=1" -o multipop_ceu_afr_one_snp_1OPA_all_SNPPicker.txt -minscore 0.4 -e multipop_ceu_afr_one_snp_1OPA_all_SNPPicker.err -defaultscore -99) > log_multi_ceu_afr_snppicker) >& log_multi_ceu_afr_snppicker.err


For Seatle SNPs gene id 2155 a SNP at position 112805968 and 112805969 were both mapped to rs3093230. 
The right answer is that  rs3093230 matches 112805969 .. but to keep things as SNPPicker found them, I deretired SNP rs3093231 and assigned it to 112805969 with a very bad score in the .PS file.

perl RunSNPPicker2.pl --random=1000000  --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU --pop=AFR --nOPA=1  --dir=SNPApp_EUR_0.90_0.05_1228_1231 --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_ceu_afr_onesnpv2_1OPA --rules="1-Inf=1" --mayobest --minscore=0.4 --default_score=-99 --hidden 

perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=CEU  --nOPA=1 --rules="1-Inf=1" --dir=SNPApp_EUR_0.90_0.05_1228_1231  --reportname=kullo_ceu_one_snp_1OPA --mayobest --minscore=0.4 --default_score=-99
perl RunSNPPicker2.pl --ps=Kullo_redo_uniq_withids_nonulls_illuminaFile_PS.csv --pop=AFR --nOPA=1 --rules="1-Inf=1" --dir SNPApp_AFR_0.90_0.05_1228_1232 --reportname=kullo_afr_one_snp_1OPA --mayobest --minscore=0.4 --default_score=-99
