GATK variant annotation
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Entering edit mode
18 days ago

Hello guys

I am annotating a vcf file using GATK VariantAnnotator. The annotation will be used in performing VQSR in next step.

my command

java -jar /mnt/x/linux/gatk-4.2.0.0/gatk.jar VariantAnnotator -R result.fa.gz -V chr1_22_GL.vcf -O gatk_annotate.vcf -A {AS_FisherStrand} -D /mnt/x/linux/test/snpEff/db/GRCh37/dbSnp/dbSnp.vcf.gz

GATK error

A USER ERROR has occurred: Unrecognized annotation name: {AS_FisherStrand}

It is a user error, i think it means the error is in my command line. IDK what it is !!!

please help $

Thank you

vcf gatk • 159 views
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1
Entering edit mode
18 days ago

remove the brackets. Just -A AS_FisherStrand

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thanks! it worked...

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