Question: How to run Beagle to impute missing data using reference panel (1000 genome)?
0
gravatar for nour.hadjz
2.6 years ago by
nour.hadjz10
nour.hadjz10 wrote:

Hi,

I'm a real beginner with beagle and i want to know how to impute on Beagle 4.1 my missing data using a reference panel. Is there a script or some commands to do this operation?

Can you help me to resolve this please ?

beagle impute software • 4.1k views
ADD COMMENTlink modified 2.6 years ago by zx87549.7k • written 2.6 years ago by nour.hadjz10
2

Did you go through the manuals?

  • beagle_4.1_21Jan17.pdf - Beagle version 4.1 documentation
  • run.beagle.27Jan18.7e1.example - a unix script which runs a short Beagle analysis
ADD REPLYlink written 2.6 years ago by zx87549.7k

hello, the script example written in the Beagle manual must be executed as is, or should I be modified? and do I execute it in the vim?

ADD REPLYlink written 2.6 years ago by nour.hadjz10

You should adapt / modify the script in the manual to suit your own files

ADD REPLYlink written 2.6 years ago by Kevin Blighe68k

ok , I will try and let you know thank you !

ADD REPLYlink written 2.6 years ago by nour.hadjz10

Hi, i work on a Macbook Pro with 16Go and i want to run Beagle using this syntax:

java -Xmx16g -jar beagle.27Jan18.7e1.jar get=sortieMSL.recode.vcf out= result ref=chr22.1kg.vcf.gz chrom=22:0-50000 impute=true

but it doesn't work i have an Error message : unrecognized parameter: sortieMSL.recode.vcf i know that i have something wrong but i dont know how to do! can you please help me with my syntax ?!

ADD REPLYlink written 2.6 years ago by nour.hadjz10

You posted this as a new question? - Running Beagle for imputation

ADD REPLYlink written 2.6 years ago by Kevin Blighe68k
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