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

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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