This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Convertf. Convert from PED to EIGENSTRAT format

I am trying to use convertf software to convert files from PED to EIGENSTRAT format. I have the following files: a.ped, a.pedsnp and a.pedind. According to the tutorial:

https://reich.hms.harvard.edu/software/InputFileFormats

I should use this command:

/bin/convertf -p parfile

I have tried different ways of running the command:

convertf a -p par.PED.EIGENSTRAT
convertf -p a par.PED.EIGENSTRAT
convertf -p a.ped a.pedsnp a.pedind par.PED.EIGENSTRAT

However, I get:

parameter file: a
Can't open file
: No such file or directory
fatalx:
can't open a
Aborted (core dumped)

I am also not sure what should be the parfile

Can someone indicate me what is the proper way of running such command?

convertf
• 5,356 views • link
updated by mathilde.andre.student • mathilde.andre.student • written by Mr Locuace Mr Locuace

1 answer

Hi,

You need to create the parfile yourself (that includes the names of the files to convert, the type of conversion and the name for the output files) following this example https://github.com/DReichLab/AdmixTools/blob/master/convertf/par.PED.EIGENSTRAT

And then you only use your parfile name in the command

Hope it helps, Mathilde

• 0 views • link
written by mathilde.andre.student • mathilde.andre.student

Log in to answer this question.

More posts like this