Human b37 Indels/dbsnp annotation versions for IndelRealigner & BaseRecalibrator

tony

Dear GATK Team,

I have recently downloaded the GATK Bundle to get the human reference genome and its associated annotations.

After the mapping step on my lane BAM files, I am planning on using IndelRealigner and BaseRecalibrator as it is explained in the "Best Practices v4".

I am always confused about which annotation file I should use for my analysis.

For the Indel realignment, in the command line arguments of RealignerTargetCreator, one have to set the '--known' switch to indicate known indel sites.

--known:indels,vcf Mills_and_1000G_gold_standard.indels.b37.sites.vcf --known:dbsnp,vcf dbsnp_135.b37.vcf

But in the annotations folder, you can also find 'dbsnp_135.b37.excluding_sites_after_129.vcf' for dbsnp (version before 1000K genomes). Depending on which one I use the target intervals files are pretty different. So I am really wondering which one should be used in my case ? Or is there any other factor that could drive me to the better choice ?

I have a similar dilemna with base recalibration, "dbsnp_135.b37.vcf" or "dbsnp_135.b37.excluding_sites_after_129.vcf" in the '-knownSites' switch ?

Thanks a lot, Best,

Anthony

Geraldine_VdAuwera

Hi Tony, Glad you found the answer to your question in the FAQs, that's what they're for!

We prefer to leave this thread up, so other users who have the same question can find your answer if they browse the forum.

tony

Actually, I found my answers in the FAQ.

Here : http://gatk.vanillaforums.com/discussion/1247/what-should-i-use-as-known-variantssites-for-running-tool-x

Is it possible to simply delete this thread ?