- Version: GATK 188.8.131.52 through Docker
- WGS 30x BAM
- 1 CPU + 64gb RAM
- ~ 3-4 days
gatk DepthOfCoverage \
--java-options '-Xmx48G ' \
-I '/path/to/generated.markduped.bam' \
-R '/path/to/Homo_sapiens_assembly38.fasta' \
-O 'NA12878' \
--intervals '/path/to/chr1.bed' ... --intervals '/path/to/chrM.bed'
I'm hoping to speed up the wall-time. I've got one interval per chromosome currently, but that can be changed if required / recommended. I asked internally about splitting the analysis up per interval, but there would be some non-trivial effort required to merge the reports and it might actually change the QC reports.
I believe the GATK3 variant of this tool could take the `-nt` or `-nct` params, just wondering if there's a planned SPARK implementation, or other tricks.
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