Right now I'm using the commands
convert_tped_to_bed="plink --noweb --tfile ${TEMP_DIR}${BASENAME} --make-bed --out ${TEMP_DIR}${BASENAME}"
convert_bed_to_ped="plink --noweb --bfile ${TEMP_DIR}${BASENAME} --recode --tab --out ${PLINK_DIR}"
to convert tped files to ped files. Is there a way to go directly from tped to ped? --make-ped does not work.
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I think you're making this more difficult than it needs to be: plink --tfile file.tped --recode
Hi,
the .tped file should be associated to a .tfam file (same name, different extension. i.e. FILE.tped and FILE.tfam), in this way you could avoid to type the extension of the file, and write just FILE.
Plink will go through both the files in order to elaborate what you need.
Plink website is very exhaustive, but have a look to this one too, if it helps: https://www.cog-genomics.org/plink2/formats
Hi,
I have also a huge tped file, and when I try to use the command plink --tfile file.tped --recode, the software returns me an error telling me that the file that I am using as input but with extension .tfam doesn't exists. This is true, but in the previous command it does not appear so I don't know where is the problem.
Hope someone can help me,
Thanks.
To read a transposed fileset, use the command
plink --tfile mydata
which implies mydata.tped and mydata.tfam exists; alternatively, if the files are differently named, they can be individually, fully specified:
plink --tped mydata.tped --tfam pedinfo.txt
HINT You can generate transposed filesets with the --transpose option, described in the data management section
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