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--intervals input in GenomicsDBImport for non model de novo genome

Dear gatk team,

I tried searching for the answer in existing threads, but could not find a definitive answer, but I am sorry if you have already answered this question! I have followed the gatk best practices for 'germline short variant discovery' and have just finished running HaplotypeCaller in GVCF mode. So far everything has worked well! I have ~150 SNP array samples (5K SNP array, from 150 individuals) that were aligned to a non-model de novo genome (~15000 scaffolds), and now have ~150 g.vcf files that I am hoping to combine using GenomicsDBImport. However, I am very unsure of the value I need to enter for the --intervals argument, as I do not have "known" chromosomes at this stage. How do I generate an interval list for a de novo genome?

Any help will be appreciated,
Many thanks to anyone who helps and kind regards,
-RG

Answers

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