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.
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written
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Kris •
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 |
+----------------------+
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.
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