Hi, I am working on joint genotyping using GenotypeGVCF with around 850 samples. Interval.list contains 8 chromosomes and several contigs. The script is running since last many days. Is there a way around to speed up this process? I asked GATK guys and they suggested me this script but don't know can I just use it for GenotypeGVCF because GenomicsDBimport is already finished. And another thing if I am using this script then interval.list is no more needed or need to be mentioned in some other way. The script by GATK guys is here:

for n in {1..19}; do

  gatk GenomicsDBImport -L $n <rest of command same as before>

  gatk GenotypeGVCFs -L $n <rest of command same as before>

done

I tried it this way: for n in {1..212};do qsub genonotypeGVCF.sh -L $n; done I have 8 chromosome and rest of the contigs (212). But it didn't work, the results output is very slow.

The GenomicsDBimport is already finished on my samples and I want to run it just for GenotypeGVCF. Is that possible?

Or I need to run both of these script together to make it faster.

How people are getting faster results with genotypeGVCF, can somebody post the scripts here?

Thanks,