Plink/howto

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Plink

Utilities to convert Illumina SNP report files to plink format are available in icb-commons/plink-adapters.

If multiple patient cohorts are genotyped with the same SNP platform, simply concatenate all the lgen files into one. 

 rm all.lgen
 cat *.lgen >all-lgen 
 mv all-lgen all.lgen
 sort -u *.samples|   awk '{print "0 "$1" 0 0 other 1"}' > all.fam 
 # create the familly info file for case-control study (use zero for parents ids so that samples are considered founders).


Convert the lgen file to binary plink format: 

 plink --lfile all  --no-sex --out all-1 --make-bed

Assign phenotype based on LOAD attribute in all-phenotypes.cov (generated by plink-adapters) 

 plink --bfile all-1 --out LOAD-vs-others --make-pheno all-phenotypes.cov LOAD --make-bed

Inspect the file 

 plink --bfile LOAD-vs-others

Calculate minor allele frequencies: 

  plink --bfile LOAD-vs-others --freq --out freqs --allow-no-sex

Association test 

 plink --bfile all-1 --out LOAD-vs-others --make-pheno all-phenotypes.cov LOAD --allow-no-sex  --assoc
 sort -k 9 -n LOAD-associations.assoc

LD calculations 

 plink --bfile all-1  --make-pheno all-phenotypes.cov LOAD --r2 --out LD  --ld-window-r2 0


Find SNPs on chromosome 10 

 plink --chr 10 --bfile all-1 --out chr10-snps --freq

Create combinations of any SNP on chromosome 10 with rs2986017 

 awk '{print "* "$2" rs2986017 "}' chr10-snps.frq > rs2986017.hlist

Impute haplotypes for each pair 

 plink --bfile all-1 --out all-haplo-rs2986017 --allow-no-sex --hap rs2986017.hlist --hap-impute

Output ends with: 

 Writing imputed ped file to [ all-haplo-rs2986017.impute.ped ] 
 Writing imputed map file to [ all-haplo-rs2986017.impute.map ]

Use haplotypes to create new markers 

 plink --file all-haplo-rs2986017.impute --make-pheno all-phenotypes.cov LOAD --out all-haplo-rs2986017-imputed-2  --make-bed

Test associations with the haplotype markers 

plink --bfile all-haplo-imputed-2 --make-pheno all-phenotypes.cov LOAD --assoc --ci 0.05 --out rs2986017-haplo-associations-ci


plink --file all-haplo.impute --out all-haplo-2 --allow-no-sex --hap rs2986017.hlist --make-pheno all-phenotypes.cov LOAD --make-bed

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low-throughput genotyping

The following converts text input files to the lgen plink format: 

 awk '{print "0 "$1" rs2986018 "substr($2,1,1)" "substr($2,3,2); }' rs2986018 > rs2986018.lgen

Input are expected in the format (where the second field indicate the genotype, e.g., C/C, C/T, T/T, or A/A, A/C, C/C) 

 patient-id [tab] A/A
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