No Pgp Data In Dbsnp?

Question

[Kris]

Am I right to assume that Personal Genome Project data has not been deposited in dbSNP?

There are genomic data (exomes / wholes sequences etc) available for hundreds of samples now through the PGP at https://my.personalgenomes.org/public\_genetic\_data yet there does not seem to be any dbSNP submitter ID corresponding to this project (all submitters are listed at http://www.ncbi.nlm.nih.gov/projects/SNP/snp_tableList.cgi?fld=Submitter+handle&cond=view+all&str=&cond=&type=submitter&fld=str&go=Search+%28case+insensitive%29&.cgifields=cond&.cgifields=fld ).

The only PGP-related dbSNP identifier I could find was http://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewTable.cgi?handle=CHURCH_CG54K , but this only consists of 6 individuals.

Does anyone know of other PGP data present in dbSNP?

Thanks.

Answer 1

[Pierre Lindenbaum]

You can find some pg% tables in the UCSC mysql database:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'show tables like "pg%"'
+----------------------+
| Tables_in_hg19 (pg%) |
+----------------------+
| pgNA12878            |
| pgNA12891            |
| pgNA12892            |
| pgNA19240            |
| pgSjk                |
| pgVenter             |
| pgWatson             |
| pgYh1                |
| pgYoruban3           |
+----------------------+

[Kris]

Thanks Pierre. I'm interested in downloading some complete genomes from the PGP, and then filtering out common variants using dbSNP.

Before doing this, however, I need to remove PGP-deposited data from dbSNP, to avoid filtering the genomes against themselves! That's why I wanted to know if the PGP data was in dbSNP or not.

It does look like most of the PGP has never been deposited though. This is a bit surprising, but does make my job easier.