GATK variant annotation

Question

[shubhamkumbhar420]

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

Answer 1

[Pierre Lindenbaum]

remove the brackets. Just -A AS_FisherStrand

[shubhamkumbhar420]

thanks! it worked...