Entering edit mode
2.8 years ago
arwa.ahmad95
•
0
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.
how your input looks; chr naming particularly.
there is no output on screen! " > " this appear like it's wait me to write more code!
just remove the last
\and run it again( -bash: gatk: command not found ) this will appear , so how can I solve the problem?
Chrom column in my input consists of Chr1 , ......