Created
June 17, 2018 23:57
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Collect gVCF files and add chrY to a GenomicsDB using GATK4.
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# 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 |
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