#the second item in the inputfile entry should match the project_id project_code #in the projects_path file for the data in that input file #input_file UDP1026 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP1026.vs.filtered #input_include_linkage_bed_file UDP1026 /gs1/users/sincanm/VarSifter/1026linkage.bed # #input_file UDP1130 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP1130.vs.filtered #input_file UDP1166 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP1166.vs.filtered #input_file UDP130 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP130.vs.filtered #input_file UDP1418 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP1418.vs.filtered #input_file UDP1706 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP1706.vs.filtered #input_file UDP1869 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP1869.vs.filtered #input_file UDP2009 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP2009.vs.filtered #input_file UDP2146 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP2146.vs.filtered #input_file UDP2248 /gs1/users/sincanm/VarSifter/incomingvsfiles/UDP2248.vs.filtered_UDP2809_asUnaffected.vs.filtered #input_file UDP2296 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP2296.vs.filtered # #input_file UDP2717 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP2717.vs.filtered # #input_file UDP2753 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP2753.vs.filtered # #input_file UDP337 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP337.vs.filtered #input_file UDP337 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP337.vs.filtered.test #input_include_bed_file UDP337 /gs1/users/sincanm/VarSifter/UDP337.include.bed #input_file UDP369 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP369.vs.filtered #input_cnv_bed_file UDP369 /gs1/users/sincanm/VarSifter/UDP369.include.bed #input_bam_file UDP369 UDP369 /gs1/users/sincanm/ngs/sequences/WE/UDP369/UDP369/UDP369.bam #input_bam_file UDP369 UDP3350 /gs1/users/sincanm/ngs/sequences/WE/UDP369/UDP3350/UDP3350.bam #input_bam_file UDP369 UDP1641 /gs1/users/sincanm/ngs/sequences/WE/UDP369/UDP1641/UDP1641.bam #input_bam_file UDP369 UDP1640 /gs1/users/sincanm/ngs/sequences/WE/UDP369/UDP1640/UDP1640.bam # #input_file UDP3755 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP3755.vs.filtered #input_file UDP3842 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP3842.MISC49.vs.filtered # #input_file UDP3866 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP3866.vs.filtered #input_include_bed_file UDP3866 /gs1/users/sincanm/VarSifter/UDP3866.include.bed # #input_file UDP4413 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP4413.vs.filtered # #input_file UDP563 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP563.vs.filtered #input_file UDP577 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP577.vs.filtered #input_file UDP606 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP606.vs.filtered #input_file UDP658 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP658.vs.filtered #input_file UDP675 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP675.vs.filtered ## #input_file UDP679 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP679.vs.filtered ## #input_file UDP755 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP755.vs.filtered #input_file UDP760 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP760.vs.filtered #input_file UDP798 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP798.vs.filtered #input_file UDP810 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP810.vs.filtered #input_file UDP860 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP860.vs.filtered #input_include_linkage_bed_file UDP860 /gs1/users/sincanm/VarSifter/UDP860linkage.bed # #input_file UDP984 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP984.vs.filtered # #input_file UDP4694 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP4694.vs.filtered #input_include_linkage_bed_file UDP4694 /gs1/users/sincanm/VarSifter/4694linkage.bed # #input_file UDP2473 /home/sincanm/sincanm/VarSifter/incomingvsfiles/UDP2473.vs #input_include_bed_file UDP2473 /gs1/users/sincanm/VarSifter/2473IBDbedfile.bed # #input_file UDP4413 /home/sincanm/sincanm/VarSifter/nextgene_input/UDP4413_Report.txt #input_file /gs1/users/sincanm/immune_disorders/MH_YA05.mpg.nonref.vs #input_include_bed_file MH_YA05 /gs1/users/sincanm/immune_disorders/Immune1_candidatYA05.bed #input_file /gs1/users/sincanm/immune_disorders/MH_YA21.mpg.nonref.vs #input_include_bed_file MH_YA21 /gs1/users/sincanm/immune_disorders/Immune2_candidatYA21.bed #enable when a new allsamples file arrives that needs to be run for hg19 annotations and seattleseq(if needed) # old input_file population /gs1/users/sincanm/VarSifter/allfams/incoming/AllGahl.all.annot.vs.corrected # old input_file population /home/sincanm/sincanm/VarSifter/allfams/incoming/AllGahl.all.annot.vs.hdrs_fxd input_file population /home/sincanm/sincanm/varmd/AllGahl.vs.hdrs_fxd-2012-06-02 #following is the path to the final allsamples file to be used, this file is automatically created after #running addhg19 steps on the population_file_fixed #population_file /home/sincanm/sincanm/VarSifter/allfams/AllGahl.all.annot.vs.hdrs_fxd_tmp/AllGahl.all.annot.vs.hdrs_fxd_withhg19_dbsnp_pop_ss_snv_indel #population_file /home/sincanm/sincanm/AllGahl.vs.hdrs_fxd-2012-04-30_tmp/AllGahl.vs.hdrs_fxd-2012-04-30_withhg19_dbsnp_pop_ss_snv_indel population_file /home/sincanm/sincanm/AllGahl.vs.hdrs_fxd-2012-06-02_tmp/AllGahl.vs.hdrs_fxd-2012-06-02_withhg19 interval 20000 nodetype norm cdpred_cutoff 400 projects_path /home/sincanm/sincanm/varmd/projects_data_2012_06_02.txt liftOver_path liftOver liftOver_chain_path /gs1/users/sincanm/public_data/hg18ToHg19.over.chain expression_snps_path /home/sincanm/sincanm/varmd/functional_snps_names_only.txt chrominfohg19_path /home/sincanm/sincanm/varmd/chrominfohg19 seattleseq_dir_path /home/sincanm/sincanm/varmd founders_file /gs1/users/sincanm/VarSifter/allfams/Founders.vs dbsnp_vcf_path /gs1/users/sincanm/public_data/hg19/dbsnp137-00-All.vcf.gz #dbsnp_db_path /home/sincanm/sincanm/varmd/dbsnp_sqlite3.db population_db_path /home/sincanm/sincanm/varmd/population_sqlite3.db variants_db_path /home/sincanm/sincanm/varmd/variants_sqlite3.db knowngene_path /gs1/users/sincanm/public_data/hg18/knownGene.txt knowntorefseq_path /gs1/users/sincanm/public_data/hg18/knownToRefSeq.txt kgAlias_path /gs1/users/sincanm/public_data/hg18/kgAlias genesToExclude /home/sincanm/sincanm/varmd/fake_genes_list.txt hg18fasta /home/sincanm/sincanm/ngs/refgenomes/hg18/hg18.mfa dbconnect mysql://sincanm:s!N