Storing Snp Data In Gff3 Format And Loading Into Chado

Question

[hansyuhans]

Hi, I'm trying to load SNP data into a Chado database by storing them in GFF3 format and then running the gmodbulkload_gff3.pl script to get them into Chado.

I'd like to have the reference and alternative bases loaded with each SNP.

Which tags should I use to store this information in the GFF3 file so that the bulk load script can correctly interpret it?

Thanks!

Answer 1

[cain.cshl]

Hi,

There aren't standard tags for marking the ref and alt bases, but a reasonable thing to do would be to use the tags that are used in GVF. The only problem is that you can't upper case the initial letter of the tags since they aren't defined as part of the GFF3 spec. So instead of something like this:

Variant_seq=A,G;Reference_seq=G;

I'd suggest this:

variant_seq=A,G;reference_seq=G;

Follow up questions should best be addressed to the Chado mailing list:

https://lists.sourceforge.net/lists/listinfo/gmod-schema

Scott