gatk4 GenomicsDBImport intervals with whole genome
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2.7 years ago
Peter Chung ▴ 190

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.

gatk intervals GenomicsDBImport • 4.0k views
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What was your reference genome?

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5
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21 months ago

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.

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