Conversion of imputed output file from beagle 4.1 to vcf dosage format
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2.3 years ago
mab658 ▴ 80

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

RNA-Seq SNP sequencing • 1.7k views
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Linked thread: Imputation of vcf file

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