I am familiar with C++, so is there a tool to implement GATK using C++ ?
system("java -Xmx5g -jar GenomeAnalysisTK.jar");
What do you mean with "implement"?
That should mean "re-code" but we have no additional context :)
That's what it means, but I don't think it's what OP means :-)
HI, It' means to re-write GATK to use C++ or other language.
GATK is a set of numerous tools using map/reduction of data. Some tools already exist as a C++ program (e.g: SelectVariants can be compared to bcftools view ).
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