cg exportplink ?options? varfile resultfilebase
make a plink "Transposed fileset" from the genome data
This command makes two files that can be used as a transposed
fileset in plink (--tfile option).
- 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.
- 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
- variant file
- result file
- -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