How about VQSR variant set if the reference not the hg38

linzlinz chinaMember

There is a question when I run GATK. My goal is get variant from multiple sample in the rice. And I get a raw variant from HaplotypeCaller, and followed CombineGVCFs, GenotypeGVCFs according to the Best Practices. All looks good, but when I attempt to filter Variants, I chose the VQSR method which is recommend by you. (Because my sample number is enough to builds a model ). The question is when I run VariantRecalibrator, I need to input some variant set which is representative of true sites. I have no idea where to download those snp set, I need your help.

By the way, My reference is rice genome.

thank you!



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