Mike;
Does your SNP pipeline recognize and assign dbSNP rs#### identifiers?
I'm interested coding better integration between galaxy and SNPedia annotations of the human genome http://www.SNPedia.com
To start, thanks for all the work you do with SNPedia. It's an excellent resource that has been invaluable for looking at disease traits. Really awesome work.
I'm hoping to ask a few pipeline related questions to anyone who's pipelines assign rs#s to nextgen data.
We use GATK's UnifiedGenotyper in our pipeline:
http://www.broadinstitute.org/gsa/wiki/index.php/Unified_genotyper
It can take a dbSNP VCF file, like the dbSNP 132 release:
ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/v4.0/00-All.vcf.gz
and assigns rs associations as the 3rd ID column of the VCF file. Here's a script with all the gory details about how we call the tools:
https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/gatk_genotyper....
The Galaxy folks likely have some good ideas about integration, but one approach could be to have a tool or display app that takes a VCF files with human genome builds and produces HTML with links to resources such as SNPedia. This would just need linkouts like http://snpedia.com/index.php/rs1234.
Brad