GenomeComb

exportplink

Format

cg exportplink ?options? varfile resultfilebase

Summary

make a plink "Transposed fileset" from the genome data

Description

This command makes two files that can be used as a transposed fileset in plink (--tfile option).

resultfilebase.tfam.pre
This file must be edited and renamed to resultfilebase.tfam: Only the names are correct. The other fields (father, mother, sex, phenotype) are set to missing (0 or -9) and must be corrected.
resultfilebase.tped
This file contains the variant and the genotype information. Variants with more than two alleles (which are not supported by plink) are skipped with a warning message. The genetic location is (very roughly) estimated by dividing the base position by 1M.

Use with plink

Edit resultfilebase.tfam.pre to the correct settings, and rename to resultfilebase.tfam You can use the files with the -tfile option, e.g. plink --tfile resultfilebase --recode12

You can use plink to recode to the default plink format (non-tansposed) plink --tfile resultfilebase --recode

Arguments

varfile
variant file
resultfilebase
result file

Options

-q query
query (as can be given to cg_select). Only variants matching the query are included in the result.
-c 1/0
code genotypes to numbers (reference = 1, alternative allele = 2).

Category

Conversion