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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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VariantAnnotator cmd line arg parsing error #4604

Open 13am opened 6 years ago

13am commented 6 years ago

Passing a .ped file to the VariantAnnotator tool does not work:

gatk4 VariantAnnotator -ped my.ped --annotation PossibleDeNovo --variant my.vcf --output out.vcf

Result: A USER ERROR has occurred: p is not a recognized option

gatk4 VariantAnnotator --ped my.ped --annotation PossibleDeNovo --variant my.vcf --output out.vcf

Result: A USER ERROR has occurred: ped is not a recognized option

Above, "gatk4" is an alias of "/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/bin/java -jar ~/lib/gatk/gatk-4.0.3.0/gatk-package-4.0.3.0-local.jar"

cmnbroad commented 6 years ago

@jamesemery I think this is because the annotation plugin, which has the pedigree arg, hasn't been integrated with the tools yet (second part of https://github.com/broadinstitute/gatk/issues/3287) ?

jamesemery commented 6 years ago

@cmnbroad That is correct. Once upon a time it was waiting on the VariantAnnotator to be integrated before advancing on it but now its being held in place by newtons first law. I will take a look at updating the branch.

lbergelson commented 6 years ago

@jamesemery Is this issue resolved now?