I am using GATK version 4.0, I tried to use multiple threads for calling variants using HaplotypeCaller using following command
gatk --java-options -Xmx90G -nt 28 HaplotypeCaller -I output.bam -R wheat_ref.fa -O final.vcf
and the error is
'-nt' is not a valid command
I have also used --num_threads but again the error was the same, as written here this parameter is available in previous versions of GATK but I don't know what's its status in current version of GATK i.e GATK 4.0. Whether it is deprecated or replaced by some other parameter?
Is there any way of calling multiple threads for variant calling with GATK 4.0?