BEAGLE 4.1 imputation

Question

[cholingken]

Hi all,

I am new to the field of imputation. I am trying to use BEAGLE v4.1 to do a imputation of a few sets of WGS and WES. 1. I would like to know what are the difference of the output of gt, gl and gtgl arguments respectively. 2. After I run gt argument second time, output from the above argument will be phased and non-missing, so this output could be the target data for the imputation? 3. If I have a multiple target data sets, how can I do a imputation of all of them with same reference data set at a time? 4. How to check the strand inconsistencies between reference and target data? If inconsistency occurs, how to make them consistent? Thank you so much for your time!

Ken

[jean.elbers]

If you would like to phase and impute a VCF file, then the following works in BEAGLE 4.0 (not sure about BEAGLE 4.1)

java -Xmx4000m -jar ~/bin/beagle.r1398.jar \
gtgl=VCF-file-that-you-want-to-phase-and-impute.vcf \
nthreads=2 \
out=VCF-file-that-is-now-phased-and-imputed

*note that BEAGLE will add *.vcf.gz to the end of the text in the out argument

[johnnythejota]

Hi, did you get the imputation? Would you help me ?