Entering edit mode
13 months 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 , ......