使用PLINK进行基因型数据质量控制与合并.pdfVIP

cdplink-1.10.2amd64-pc-linux/

Tocheckandcleanupmissingnessgenotypes,MAFlowqualitycalls,ME

errorandHWE:

./plink--file/picb/humpopg7/BPHoh/Dengue_output/birdseed.calls--geno0.1--

mind.1--maf0.05--hwe0.002--me0.050.1--recode--out

/picb/humpopg7/BPHoh/cleaned--noweb

Tocheckwiththeallelefreqstats:

./plink--file/home/boonpeng/Downloads/plink-1.07-x86_64/cleaned_Dengue--

outfreq_stat

TolisttheSNPs:

./plink--file/home/boonpeng/Downloads/plink-1.07-x86_64/cleaned_neg--list

[toexcludegenderfromtheanalysis:--allow-no-]

ToexcludetheSNPs{duplicationmarkerswasfound}:

./plink--file/home/boonpeng/Desktop/affy6_output/birdseed.calls--exclude

/home/boonpeng/Documents/duplicate_SNP.txt–noweb

Tomerge2PLINKfi:

./plink--file/home/boonpeng/Downloads/plink-1.07-x86_64/cleaned_Dengue--

merge/home/boonpeng/Downloads/SGVP.MAS.calls.ped

/home/boonpeng/Downloads/SGVP.MAS.calls.map--recode--out

merge_dengue_SGVP_MAS–noweb

GeneticAssociation{afterwhichdatahasbeenQC’ed):

./plink--file/picb/humpopg7/BPHoh/plink-1.07-x86_64/plink--pheno

/picb/humpopg7/BPHoh/plink-1.07-x86_64/my.pheno.txt--assoc–noweb

withpermutationtest(defaultsetting):

./plink--file/picb/humpopg7/BPHoh/plink-1.07-x86_64/plink--pheno

/picb/humpopg7/BPHoh/plink-1.07-x86_64/my.pheno.txt–-assoc--perm-–noweb

MDSplotandpopulationstratification:

./plink–filemyfile–cluster

./plink--file/picb/humpopg7/BPHoh/Malay/3popMly--genome--out

/picb/humpopg7/BPHoh/Malay/3popMly_data--noweb

./plink--file/picb/humpopg7/BPHoh/plink-1.07-x86_64/My_Dengue/plink_QC--

read-genome/picb/humpopg7/BPHoh/plink-1.07-

x86_64/My_Dengue/My_Dengue.genome.genome--cluster--mds-plot2--noweb