[Feedback] Site Feedback: Rice NCBI dbSNPs

[feedback at gramene.org]

URL         : http://www.gramene.org/

Subject     : Site Feedback: Rice NCBI dbSNPs

Name        : Surya

Email       : nextgenseq.bioinfo at gmail.com

Organization: UCLA

Comments    : 

Hi,
I have been working with a strain of Rice and have mapped the reads to the Nipponbare assembly v7.0 from MSU. I am looking for all annotated variants from the various Rice cultivars studies (inc variants with indica spp) using arrays and sequencing projects done so far. I looked into getting  NCBI dbSNP although the VCF files they put out doesn't match the MSU Nipponbare assembly. Perhaps, it was mapped to the RAP build.

I realize Ensembl has a set of variants they derived from NCBI dbSNP
although these are also mapped to the IRGSP1.0 assembly GCA_000005425.2
http://plants.ensembl.org/Oryza_sativa/Info/Annotation#variation

Is there an equivalent VCF file(s) for the Nipponbare assembly from MSU?

I noticed you have the 400K core SNPs from the Rice 3K genomes project mapped to the MSU7 build and wondering if you have mapped the NCBI dbSNP as well.

Thanks,
Surya


http://www.warelab.org/bugs/view.php?id=5124