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moiexpositoalonsolab / grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
http://grene-net.org
GNU General Public License v3.0
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Feature request: GenomicsDBImport #55

Open DuttaAnik opened 2 months ago

DuttaAnik commented 2 months ago

Hi, Thanks for developing the tool. I was wondering whether it is possible to include GenomicsDBImport after running the GATK Haplotypecaller for SNP calling. Because for thousands of samples, I found GenomicsDBImport to be more efficient than CombineGVCFs.

Thanks.

lczech commented 2 months ago

Hi @DuttaAnik,

thanks for the suggestion! That seems like a good idea and is not overly complicated to integrate. Unfortunately, I won't have time for this right now, but I could try to work on it in a bit. Alternatively, if you want, feel free to contribute this to grenepipe yourself as well ;-)

Let's keep this issue open for now, and let's see what we can do about this.

Cheers and so long Lucas