Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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    Alexandria Pinto

    The attached links in this article are broken, specifically the FAQ link that you reference for us to follow. Can you provide a functioning link for that information?

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    Jacob Shujui Hsu

    I can confirm that the links for VQSR are still missed (May 2021). 

    Also, I found a VQSR parameter discrepancy for omni dataset usage.

    Some previous GATK3 posts indicate the setting for omni and here 

    --resource:omni,known=false,training=true,truth=true,prior=12.0

    Here is the parameter I found in this post :

    --resource:omni,known=false,training=true,truth=false,prior=12.0

     

    Q1: Why are they different? I can not find any post discussing this issue. 

    Q2: Because of the discrepancy above, the parameter recommendations would be needed more than ever. I can not even find the para recommendation for INDEL. 

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