how to convert data from PLINK to BEAGLE

[ShirleyLiu]

Dear all,

I have some problems when convert data from PLINK (PED,MAP) to BEAGLE Genotypes file format.

There is a pipeline provided by GERMLINE software (http://www1.cs.columbia.edu/~gusev/germline/), which helps to convert. However I got some errors which I am not sure how did it happen and how to solve it.

I have followed the README for each step. The only thing I have change from transformation script is the input path. Before I changed the path, errors were more.


Here is error:
Exception in thread "main" java.lang.IllegalArgumentException: missing out argument
at c.d.a(Unknown Source)
at c.d.a(Unknown Source)
at phaser.Z.<init>(Unknown Source)
at phaser.PhaseMain.<init>(Unknown Source)
at phaser.PhaseMain.main(Unknown Source)
ERROR: out.pre_phase.bgl.phased does not exist or is empty

[ShirleyLiu]

no one answer?

[ShirleyLiu]

keep on asking

[mpiro]

This should do:
./ped_to_bgl [ped file] [map file] > out.bgl

[ShirleyLiu]

This should do:
./ped_to_bgl [ped file] [map file] > out.bgl

Thank you for your answer. I have got a converted file , however more problem came out. For example, this mendelian error problem...

[Daniel E. Weeks]

The free Mega2 program will convert from PLINK format to BEAGLE format.

[chrchang]

PLINK 1.08p actually has an undocumented --recode-beagle flag which does this.