Question: Conversion of imputed output file from beagle 4.1 to vcf dosage format
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gravatar for mab658
2.1 years ago by
mab65880
mab65880 wrote:

A filtered VCF file has been successful imputed using beagle 4.1 as follows:

java -Xmx24g -jar /programs/beagle41/beagle41.jar gt=/workdir/moshood/snps/snp_filtered.vcf.gz.recode.vcf nthreads=8 niterations=0  out=imputed_file

The output file named impute_file is phased and imputed. Could anyone guide me on appropriate software to use for converting the imputed file to dosage VCF format so that I could use it for further analysis? I would need the script as well. Thanks

sequencing snp rna-seq • 1.5k views
ADD COMMENTlink modified 2.1 years ago by _r_am32k • written 2.1 years ago by mab65880

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink written 2.1 years ago by _r_am32k

Linked thread: Imputation of vcf file

ADD REPLYlink written 2.1 years ago by Kevin Blighe69k
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