2017暑期班课件plinkcourseQC-第四课-晚上.pptxVIP

Using PLINK for data quality control (QC) in whole genome association study (Day one, handout exe);Tools and configuration;Source of error;Section 1: Using Q-Q plot to overview of the data quality;--qq-plot;OUTPUT: wgas1.assoc.adjusted;;Section 2: Removing poor genotyped SNPs;# To test the missing rate, use option --missing plink.exe --noweb --file wgas1 --missing #This option creates two files: #plink.imiss #plink.lmiss ;OUTPUT: plink.imiss/plink.lmiss;HWE;OUTPUT: plink.hwe;Minor Allele Frequency (MAF);genotyping rate;;Family data: Mendel Errors; # If the study is a family-based design