gravatar for dharaawasthi

2 hours ago by

Indian Institute of Technology, Jodhpur

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?



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