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

Contamination calculated with and without matched-normal differ from each other



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    Bhanu Gandham

    Hi ,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

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    David Benjamin

    Pubudu Saneth Samarakoon I think your commands for GetPileupSummaries may be incorrect.    The -variant argument as in the tutorial should be the "small_exac_common" vcf provided in the GATK best practices google bucket (gs://gatk-best-practices/) (I can't tell what ${pileup_summaries} means in your commands).  The -intervals argument should usually not be specified ie you usually want to calculate contamination over the entire bam file.

    To answer your other question, you should use the matched normal when you have it.  It can never hurt.

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