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Obtain VCF format file from imputed dosage format file using beagle2vcf

Please how do I use this expression to convert imputed snps data in dosage format to VCF format

java -jar beagle2vcf.jar [chrom] [markers] [bgl] [missing] > [vcf]

An example will give me a better understanding. I don't understand what the option [markers], [bgl], and [missing] actually stand for? where do I specify name of my input file, and what genotype and marker files to use?

snp
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updated by kas • kas • written by mab658 mab658

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

Also, please proof-read your posts to check for typos when you post - it always helps :-)

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written by Ram Ram

1 answer

have you got any solution? I'm also searching for this

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written by kas • kas

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