how/where to download resource vcf files

genaro_pimienta

Hello, I am having a hard time finding the resource vcf files, needed for VariantRecalibration.

hapmap_3.3.b37.sites.vcf
1000G_omni2.5.b37.sites.vcf
dbsnp_135.b37.vcf

I don't seem to find them in the GATK bundle, as suggested:

http://gatkforums.broadinstitute.org/discussion/1215/how-can-i-access-the-gsa-public-ftp-server

Any help appreciated Thanks, G.

Geraldine_VdAuwera

That's not the right place to look. Follow the instructions in the post you reference, and log into the FTP server using a proper client (not a web browser) with the appropriate login credentials. Then you will find the bundle directory.

Geraldine_VdAuwera

This tells you which human genome reference the dataset was originally aligned to before calling variants. You should always use the version of the resource that was aligned to the same reference as your dataset. Most of our resources and examples come from data aligned to b37, so if you haven't aligned your data yet and don't have any other constraints (e.g. other preexisting resources or collaborators who already work with hg19) I would recommend using our b37 genome reference (also in the Bundle).

Geraldine_VdAuwera

Are you having trouble finding the bundle itself, or just navigating the contents?

genaro_pimienta

I went to ftp://ftp.broadinstitute.org/distribution/gsa/ and downloaded gatk_resources.tgz. I see no vcf file in this folder. I also checked ftp://ftp.broadinstitute.org/distribution/HapMap3 and ftp://ftp.broadinstitute.org/distribution/human_SNP_releases. Am I missing something? Thanks, G.

genaro_pimienta

Thanks for your answer Geraldine. I have one last question. The example in http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_VariantRecalibrator.html has the files contained in the b37 folder right? What is the difference between these and the hg19 folder?. Thanks again, G.