Genomecomb moved to github on https://github.com/derijkp/genomecomb
with documentation on https://derijkp.github.io/genomecomb.
For up to date versions, go there. These pages only remain here for the data on the older scientific
application (or if someone really needs a long obsolete version of the software)
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.
Variant genotypes for samples that have a "u"
(unsequenced) in the sequenced field (or in the zyg field if no
sequenced filed is present) are set to 0 (unknown genotype) in the
plink file.
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).
- -samples samples
- Only write data for the given samples to the file, if a
sample is not present in the varfile, all genotypes will be set to
0
- -all 0/1
- Also include genotypes of samples that have a "u"
in the sequenced or zyg field. Default is 0, but if no sequenced or
zyg field is present in the file, it is 1 (i.e. all genotypes are
included)
Category
Analysis
