nextgen snp calling with dbSNP rs#s
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 Probably this should be done as a sort of https://bitbucket.org/galaxy/galaxy-central/wiki/DataSources I'm hoping to ask a few pipeline related questions to anyone who's pipelines assign rs#s to nextgen data. -- -- Mike Cariaso http://www.cariaso.com
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
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.
Exactly the sort of info I was looking for. I'd not known of Unified genotyper but am pleased to see open code and a wiki manual. Happily Promethease already knows how to read VCF http://snpedia.com/files/promethease/outputs/genome_1KG_pilot2_CEU_NA12891.h... Hat tip to Daniel MacArthur for drawing my attention to the format early on. 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.
Once you have an rs# assigned, guessing the SNPedia page name isn't hard enough to justify any code. There would be value if it can also resolve the strand. http://www.snpedia.com/index.php/Ambiguous_flip I'm thinking about a SNPedia hosted service for running Promethease directly from galaxy, and returning a suitably structured response for further processing. But it's very early in my thinking. -- -- Mike Cariaso http://www.cariaso.com
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Brad Chapman -
Mike Cariaso