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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Haplotypecaller running in parallel for each chromosome
I would like to run haplotypercaller with -ERC GVCF on each chromosome in parallel. Then run GenotypeGVCFs.
Do I need to first concatenate the results from each chromosome in sample1.chr_merged.g.vcf ... files then run GenotypeGVCFs with sample1.chr_merged.g.vcf , sample2.chr_merged.g.vcf .... or is it possible to run GenotypeGVCFs directly?