VariantsToTable not working

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Arwa Ahmad

• February 25, 2022 08:56

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 

 

And this error that appear to me:

( -bash: gatk: command not found ) 

I didn't know why and how to solve it?

Can u help me please? I'm newer in the field and in the GATK

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• 

  Arwa Ahmad

  • February 26, 2022 12:01

  Can any one help me?

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  Genevieve Brandt (she/her)

  • March 09, 2022 23:59

  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

  Best,

  Genevieve

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