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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

Is BQSR accurate on Novaseq 6000?

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    Genevieve Brandt (she/her)

    Hi Tom van den Bosch, I think the forum thread you linked to was referring to this article on the legacy forum, there is a discussion in the comments regarding NovaSeq data. For the actual content of the article, we have a newer version on our current website at this updated link.

    You are seeing this big change because NovaSeq uses only 4 quality bins. BQSR adjusts based on the empirical base quality and so you may see the quality decrease. Look for the quality score accuracy, which should increase after BQSR.

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    Tom van den Bosch

    Thank you very much! I will look at the quality score accuracy.

    I knew about the binned quality scores in NovaSeq, I just did not expect the quality score to drop that much after recalibration as I was used to hiseq data where the difference is usually smaller. It seems like variant calling output is what I expected so that is also a confirmation that the pipeline is working.

     

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    Genevieve Brandt (she/her)

    Thanks for the update Tom, glad the results look as expected!

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