Conversion of imputed output file from beagle 4.1 to vcf dosage format
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
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Please use the formatting bar (especially the
codeoption) to present your post better. I've done it for you this time.Linked thread: Imputation of vcf file