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

Different read statistics for a common control sample in two Mutect2 runs



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    David Benjamin

    Roman Jaksik You're right that active regions can theoretically affect this but that you shouldn't expect such a big difference.  I think that the bigger factor here is that the different tumors are yielding different assembled haplotypes.  The annotations that look like 1:229654515_C_A in your VCF are phasing tags, and you can see that they are different from one run to another.

    If your pipeline demands consistency you can generate a single assembly for the normal and both tumors in Mutect2's multi-sample mode, where in a single command you specify -I normal.bam I tumor1.bam -I tumor2.bam -normal G4_C -f1r2-tar-gz joint-f1r2.tar.gz etc.  You can do this for an arbitrary number of tumor and normal samples from the same individual.

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    Roman Jaksik

    Thank you David. I will try this out.


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