About the -d <dbSNP VCF>, is it necessary?

[wangnan9394]

Hi,
dv-trio is a good tools for variants calling!And there is not have a golden standard database as an input in other species. Like me, i research on plant genome. How could we create a dbSNP VCF file?
Thank you!
Bests,
Nan

[eipVCCRI]

Hi Nan,

In the human genome scenario, the dbSNP VCF is used to highlight common SNPs / reported SNPs, so is useful. I understand for other species, this kind of SNP database may or may not exist.

The information used from the dbsnp VCF file is the ID field

#CHROM POS ID REF ALT QUAL FILTER INFO
chr1 10230 rs775928745 AC A . . RS=775928745

If you have a database for your species, you could create a VCF with the ID of rs(your species SNP id). Use the human dbsnp as a template, location can be found in the testing-README.md.

I can see your point about -d being optional and will think about updating dv-trio to reflect that.

Thanks.
Eddie