GenomicsDBImport: large intervals can not be processed

shalabhsuman / variantCallingPipelineGermlineHC4

Germline Variant Calling Pipeline

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GenomicsDBImport: large intervals can not be processed #3

Open shalabhsuman opened 5 years ago

shalabhsuman commented 5 years ago

Currently, GenomicsDBImport has no way to take in large interval/BED files to process the gvcf merging step. One option would be to perform it on individual chromosomes. Will need to investigate more

shalabhsuman commented 5 years ago

Found this on GATK forum about this issue: https://github.com/broadinstitute/gatk/issues/3269