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

I am having problems with the BaseRecalibrator during the running process


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    Gökalp Çelik

    Hi Foad Hosseini

    BQSR without any public variant dataset is still possible with a method we name as bootstrapping. 

    Our BQSR documentation summarizes this method under the No  excuses part. 

    Basically you need to call variants from your uncalibrated bam file and select very high quality variants. Using these variants you can perform a first round of BQSR and check covariates and see if you are reaching a convergence where your reported quality scores are getting closer to empirical scores. You can repeat calling and recalibrating steps multiple times to reach convergence. Keep in mind that if your samples have too much heterogeneity then reaching a convergence may become harder. 

    I hope this helps. 

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