I am doing GWAS analysis on HapMap3 data. I used this command:
./plink --bfile HapMap_3_r3_1 --geno 0.2 --make-bed --out HapMap_3_r3_2
I got this output:
Reading map (extended format) from [ HapMap_3_r3_1.bim ] 1457897 markers to be included from [ HapMap_3_r3_1.bim ] Reading pedigree information from [ HapMap_3_r3_1.fam ] 165 individuals read from [ HapMap_3_r3_1.fam ] 112 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 56 cases, 56 controls and 53 missing 80 males, 85 females, and 0 of unspecified sex Reading genotype bitfile from [ HapMap_3_r3_1.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 1457897 SNPs 112 founders and 53 non-founders found 225 heterozygous haploid genotypes; set to missing Writing list of heterozygous haploid genotypes to [ HapMap_3_r3_2.hh ] Total genotyping rate in remaining individuals is 0.997378 0 SNPs failed missingness test ( GENO > 0.2 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 1457897 SNPs After filtering, 56 cases, 56 controls and 53 missing After filtering, 80 males, 85 females, and 0 of unspecified sex Writing pedigree information to [ HapMap_3_r3_2.fam ] Writing map (extended format) information to [ HapMap_3_r3_2.bim ] Writing genotype bitfile to [ HapMap_3_r3_2.bed ] Using (default) SNP-major mode
It says it has written the files HapMap_3_r3_2 but I can't see them. I tried ls -lh but I can't see these files. Can anyone tell me what's wrong?
