Collect gVCF files and add chrY to a GenomicsDB using GATK4.

build_cohort.rb

# Very basic Ruby script that collects all the gVCFs in a directory, and puts the results
# into a GenomicsDB for later genotyping.  The batch size is limited to 200 files at a time
# since memory usage is quite demanding.  This currently consumes 18GB of RAM on a Fedora 28
# workstation.  Reader threads does not appear to have significant impact.  

# TODO: Parameterize the contig, since GenomicsDBImport doesn't support multiple
# chromosomes at present.

command = "gatk --java-options \"-Xmx32g -Xms32g\" GenomicsDBImport \\\n"
command += "-R /mnt/genomics/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa \\\n"
Dir.glob('*.vcf.gz') do |file|
	command += "--variant #{file} \\\n"
end
command += "--genomicsdb-workspace-path /mnt/genomics/chrY \\\n"
command += "-L chrY --reader-threads=8 --batch-size 200"

exec command