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,
