gatk
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Rc vs 1365 hatcher testing parquet
TODO: Builder method Still want to fully test the compressed location method (do we? do we care about this for Azure?!??!) Still want to fully test the header creation
to run this locally:
java -jar ../build/libs/gatk.jar
CreateVariantIngestFiles
-V HG00405.haplotypeCalls.er.raw.vcf.gz.rb.g.vcf.gz
-L wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list
-IG FORTY
--force-loading-from-non-allele-specific false
--ignore-above-gq-threshold false
--project-id gvs-internal
--dataset-name hatcher_import_test
--enable-reference-ranges true
--enable-vet true
--enable-vcf-headers true
--output-type PARQUET
-SN SM-N58BO
-SNM sample_map.csv
--ref-version 38
--skip-loading-vqsr-fields false