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

Do BQSR ignore VCF sites marked as filtered, or must they be removed from the file?

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    Bhanu Gandham

    Hi mk

     

    This is a very old post and since then we have had many versions of GATK. Please upgrade to the latest version and post the tools that you used, version, exact commands and records of problematic variants so we can troubleshoot the issue.

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    mk

    Hi, thank you for your reply. There is no troubleshooting required. The question is whether the BQSR tool ignores variants that are filtered or not.

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    Bhanu Gandham

    Hi mk

     

    You will need to remove variants using SelectVariants. I don't think BaseRecalibrator ignores variants marked as filtered. 

     

    Sorry about misunderstanding your question. I hope this helps.

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    mk

    Thank you!

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