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

Which training sets arguments should I use for running VQSR? Follow

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    Jacob Shujui Hsu

    Dear development team, 

    I found a VQSR parameter discrepancy for omni dataset usage.

    Some previous GATK3 posts and this post indicate the setting for omni  as below

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

     

    However, 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, parameter recommendations would be needed more than ever.  

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