How to run Beagle to impute missing data using reference panel (1000 genome)?

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6.7 years ago

nour.hadjz ▴ 20

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 ?

software impute beagle • 9.2k views

ADD COMMENT • link updated 6.7 years ago by zx8754 12k • written 6.7 years ago by nour.hadjz ▴ 20

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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 REPLY • link 6.7 years ago by zx8754 12k

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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 REPLY • link 6.7 years ago by nour.hadjz ▴ 20

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

ADD REPLY • link 6.7 years ago by Kevin Blighe 88k

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

ADD REPLY • link 6.7 years ago by nour.hadjz ▴ 20

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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 ?!