gatk4 GenomicsDBImport intervals with whole genome

Question

[Peter Chung]

I am new in gatk tools, I would like to use GenomicsDBImport to merge GVCFs from multiple samples with whole genome. -L interval is a required option for GenomicsDBImport. For example, -L chr20 for contig chr20. -L chr20:1-100 for contig chr20, positions 1-100.

However, I would like to import whole genome (chr1-chr22) to the database. I tired chr1,chr2, it showed error as follows:

A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chr1,chr2" is not valid for this input.

I want to know any ways to import all the chr into a database by GenomicsDBImport.

[efazeln]

What was your reference genome?

Answer 1

[WouterDeCoster]

It's quite absurd that you cannot just omit this argument to run this genome-wide. You can specify an intervals.list file for the -L argument, which could look like:

chr1
chr10
chr11
chr12
chr13
chr14

or similar, as such covering the entire genome.