DosageConvertor - convert dosage vcf files to plink for PRSice2

[Sara Wennersten]

Hi, I'm new here so I hope I'm doing this right.

Has anyone used DosageConvertor to convert their TOPMed/Michigan Imputation Server output dosage.vcf files to plink binary files? I would like to convert these to plink binary files so I can use them as input for PRSice2.

I keep getting this error when I try to run the install.sh file in the DosageConvertor folder:

"Error: cget not installed. Please run 'pip install --user cget'." 

This is an error generated from the install.sh lines:

rm -rf cget/ release-build/ install.log
if [[ ! $(which cget) ]]; then
(>&2 echo "Error: cget not installed. Please run 'pip install --user cget'.")
exit -1

I have cget installed, along with updated versions of other modules, so I'm stuck here. Has anyone else had this issue and worked through it?

Thank you!

Sara

[Christopher Chang]

Note that plink2 --vcf has all the functionality you need for this.

[Sara Wennersten]

Thank you for your response. I will probably just use that. So it converts the chr#.dosage.vcf files to plink binary?

Thanks again.

[Christopher Chang]

Yes.

Note that the basic plink 1.x binary format supported by PRSice2 cannot store dosages.  If you do want to use the dosages, run

  plink2 --vcf <input filename> dosage=DS --export bgen-1.2 --out <output filename prefix>

to convert to .bgen instead.

[Sara Wennersten]

Will do. I am still very new at all of this, so I appreciate your time and input. Thank you so much!

[Sara Wennersten]

would this work for plink 1.9? if so, what version of bgen should be used?

Thanks!

Sara

[Christopher Chang]

Not if you want to keep dosages.

[Sara Wennersten]

Got it. Thank you. I have access to plink1.9 and I'm having issues installing plink2 but I will keep working on getting plink2 installed.