GenomicsDBImport support for bed files

broadinstitute / gatk

Official code repository for GATK versions 4 and up

https://software.broadinstitute.org/gatk

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GenomicsDBImport support for bed files #4013

Open huangl07 opened 6 years ago

huangl07 commented 6 years ago

dear GATK4 helper:

does GATK4 could use the same method to GenotypingGvcfs like GATK3.7?

I have try the GATK4 GenomicsDBImport but it turns out More than one interval specified. The tool takes only one?

I have aboult 10k or more scaffolds cause the poor assembly result ?

how could it be ?

lbergelson commented 5 years ago

The newest release of gatk supports multiple intervals in GenomicsDBImport. There's a known issue https://github.com/broadinstitute/gatk/issues/4994 which prevents the use of large interval lists. It should be be fixed in the next release.