@----------------------------------------------------------@ | PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| | For documentation, citation & bug-report instructions: | | http://pngu.mgh.harvard.edu/purcell/plink/ | @----------------------------------------------------------@ Skipping web check... [ --noweb ] Writing this text to log file [ india_paper_data_dbSNP-b131_pos-b37_1KG_strand.log ] Analysis started: Wed Jan 9 01:58:28 2013 Options in effect: --bfile /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH --noweb --keep india.ind --geno 0.05 --make-bed --out india_paper_data_dbSNP-b131_pos-b37_1KG_strand Reading map (extended format) from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.bim ] 1282089 markers to be included from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.bim ] Reading pedigree information from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.fam ] 3828 individuals read from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.fam ] 0 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 0 cases, 0 controls and 3828 missing 2648 males, 923 females, and 257 of unspecified sex Warning, found 257 individuals with ambiguous sex codes Writing list of these individuals to [ india_paper_data_dbSNP-b131_pos-b37_1KG_strand.nosex ] Reading genotype bitfile from [ /ebc_data/chipdata/Master_data/Master_ATGC-out_1KG_strand_730KJ_1M_730e_610K_660K_650K_Evol36_HGDP_GIH.bed ] Detected that binary PED file is v1.00 SNP-major mode Reading individuals to keep [ india.ind ] ... 142 read 3686 individuals removed with --keep option Before frequency and genotyping pruning, there are 1282089 SNPs 142 founders and 0 non-founders found 300 heterozygous haploid genotypes; set to missing Writing list of heterozygous haploid genotypes to [ india_paper_data_dbSNP-b131_pos-b37_1KG_strand.hh ] Total genotyping rate in remaining individuals is 0.490544 743167 SNPs failed missingness test ( GENO > 0.05 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 538922 SNPs After filtering, 0 cases, 0 controls and 142 missing After filtering, 125 males, 16 females, and 1 of unspecified sex Writing pedigree information to [ india_paper_data_dbSNP-b131_pos-b37_1KG_strand.fam ] Writing map (extended format) information to [ india_paper_data_dbSNP-b131_pos-b37_1KG_strand.bim ] Writing genotype bitfile to [ india_paper_data_dbSNP-b131_pos-b37_1KG_strand.bed ] Using (default) SNP-major mode Analysis finished: Wed Jan 9 02:01:22 2013