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Feb 13, 2019 · While GATK 4 is able to run on a wider range of Amazon instances, the overall runtime is much larger compared to elPrep 4. The fastest run with GATK 4 takes over 17.5 hours on m5.12xlarge and costs 48.71$, whereas the elPrep 4 run takes a bit less than 3 hours and costs only 16.25$ on m5.24xlarge, being almost 6x faster for 3x less money. Command lines in bcbio for best practice GATK calling. Standard calling, plus gVCF-based joint calling - gatk-hc-joint.log Merge multiple vcf files in a single one. Vcf file must be provided as strings (with full or relative paths). Value. Data.table/data.frame object with merged vcf files.gatk HaplotypeCaller -R $ref -ERC GVCF, then run "gatk GenotypeGVCFs -R $ref -V s1.gvcf -V s2.gvcf -V s3.gvcf" I understand that the first option might be the least preferred because it skipped the BAM files and simply merge the VCF files.