GATK Guide Book

The User Guide on line at this URL
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Example command for generating calls at all sites
-o my.vcf \
--out / -o ( VariantContextWriter with default value stdout )
File to which variants should be written. A raw, unfiltered, highly sensitive callset in VCF format.

In my hands -o my.vcf produces an error message, complaining that there is no --out
while --out my.vcf works without error

Any suggestions?


Best Answer


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