VariantsToTable not produce output file
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2.4 years ago

Hello. I want to use VariantsToTable tools in GATK Thus I write this code and it's run without an error but not produce any output file!

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 \ 
>   

So, what's wrong? Also, how I get the outputfile! Thanks.

VariantsToTable GATK • 1.0k views
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how your input looks; chr naming particularly.

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there is no output on screen! " > " this appear like it's wait me to write more code!

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just remove the last \ and run it again

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( -bash: gatk: command not found ) this will appear , so how can I solve the problem?

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Chrom column in my input consists of Chr1 , ......

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