Help: Beagle 4 Phasing

Question

[thukral.sonal]

Hello Everyone,

I am a newbie to BI and this is my first project so please bare with me. I was wondering if anyone has worked with Beagle 4 before and can help me with phasing data(mother-daughter duos)?

I have my data in plink format and after struggling with it for a week I have it in VCF format too. Beagle 4 does not have a good documentation and if you can give me any tips/advice it'll be great.

Let me know if you need more information.

-Thanks

Answer 1

[Zev.Kronenberg]

BEAGLE has extensive documentations that can be found here:

http://faculty.washington.edu/browning/beagle/beagle_3.3.2_31Oct11.pdf

What are your specific questions?

[moxu]

I googled here. :)

Suppose you have a 23andme format file, could you please give step by step instructions on how to do imputation with eagle?

Thanks much!

[jpablo]

Beagle tooks a .VCF as input, you need to convert the 23andme file to VCF.

You can achieve the conversion with bcftools something like this:

bcftools convert --tsv2vcf inputfile -f assembly.fa -s samplename -o outputfile.bcf

(assembly.fa is the human assembly GRCh37)

then you need to convert from BCF to VCF:

bcftools view outputfile.bcf > outputfile.vcf