To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Training data for VQSR step


I want to run VQSR for my Exome data. I have finished with data pre-processing and joint genotyping. Now, I want to move to the next step which is VQSR (still in the first step, VariantRecalibrator). I noticed that I don't have the training set for the tools parameter's input. Where can I download the vcf file that I need to run this command? This is what I've tried:

Hapmap (Link)
I tried to open HapMap website and I found allocated SNPs download link. Is this the file I need? The file are in XML format and splitted per chromosome and it based in Hg35. Do I need to join these XML and then convert it to VCF using GATK? Will it give some problem with the different HG build (I use HG38)

1000genome (Link)
I found the VCF file also per chromosome. I think I just need to join it, don't I? probably you can give some suggestion how to join it properly?

I don't know where I can get this file.

I think I already have this file. I have use it during the GATK pre-processing step. It is the same file, right?

Thank you for your help.


Best Answer


Sign In or Register to comment.