Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

dbSNP - ancestral_allele and gene_name data missing in SubSNP table

messiemessie Skaneateles, nyMember
edited January 2014 in Ask the GATK team

Question on the dbSNP database. Looks like the SubSNP table is the only location for ancestral_allele and gene_name information for a given snp_id/subsnp_id. However, these fields in SubSNP are very sparsely populated. For example, if you search the dbSNP web page :

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs5

you can see the ancestral allele for rs5 is G. However, if you search snp_id=5 in the SubSNP table, both ancestral_allele and gene_name are null:

mysql> select gene_name,ancestral_allele from SubSNP where snp_id=5;
+-----------+------------------+
| gene_name | ancestral_allele |
+-----------+------------------+
|           |                  |
+-----------+------------------+
1 row in set (0.00 sec)

Can anyone explain this discrepancy or know where I can get ancestral_allele or gene_name if not in SubSNP directly ?

Post edited by Geraldine_VdAuwera on
Tagged:

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    I have no idea what the SubSNP table is so I can't help you. Perhaps someone from the community will pop up with an answer, but if not I would ask the dbSNP support folks, or post your question on a more general forum like Biostars or SeqAnswers. Good luck!

Sign In or Register to comment.