VariantsToTable not workingAnswered
I have an annotated vcf file , I want to use Varianttotable tools in Gatk to extract data in vcf file to table.
Especially, I want to split the data in (info) in vcf file and save all other data in the table.
This my code :
cd /app/GATK-4.1.4/ gatk VariantsToTable \ > -V /myfiles/COPY-filter.vcf \ > -F CHROM -F POS -F TYPE -GF AD \ > -O /myfiles/output.table
Can any one help me?
Hi Arwa Ahmad,
Thank you for your patience, we have had a lot of questions on the GATK forum recently. It looks like you have not correctly called the gatk program. Either the program is not in your path or you have not installed GATK properly.
Please see this quick start guide for details about how to download GATK: https://github.com/broadinstitute/gatk#quick-start-guide
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