Known SNPs for rice for Base recalibration using GATK

Question

[Floydian_slip]

Hi,

I am analyzing rice samples for SNP detection using GATK, and for the base recalibration, I need a set of known sites for rice. For human that is usually dbsnp141.vcf available at the DBSNP ftp site (for human): ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/

I was wondering if I could the VCF files for rice (rice_4530 in the same list, Oryza Sativa, which is the rice species that I am analyzing)

ftp://ftp.ncbi.nih.gov/snp/organisms/rice_4530/VCF/

Can I use the VCF file in the link above as the know sites (or gold standards)? Are there additional VCFs out there that I can use?

Thanks.

[Ashutosh Pandey]

This should work and should be good enough. Base recalibration is not going to bring any drastic difference in the results unless your sequencing data is real bad.

[deepti1rao]

This link does not contain anything.

ftp://ftp.ncbi.nih.gov/snp/organisms/rice_4530/VCF/

Where can I find known rice snps (indica and japonica, both)

Answer 1

[Coryza]

From the University of Sydney (http://sydney.edu.au/engineering/it/research/conversazione_2009/wangt.pdf):

Oryza sativa spp.Indica and Oryza sativa spp.Japonica EST data sets were downloaded from National Centre for Biotechnology Information dbEST (Mar - 2009). These datasets contain 106,532 and 833,672 ESTs, respectively. The Single Nucleotide Polymorphism database (dbSNP) was downloaded from NCBI (rice_4530) for data verification.

rice_4530: Oryza sativa, rice_4536: Oryza nivara

So my best guess is that it would fit fine for your dataset.

[sukesh1411]

Hi

Am also working on rice genome. Can i use snps from the below database to perform base recalibration?

http://www.oryzasnp.org/_download.zul/Nipponbare