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 need to identify only the somatic mutants in the tumor by normalising the variants in the PBMC DNA(considering it as a germline variation source). I used GenomicsDBImport to call PON. but gatk Mutect2 doesnot take pon from GenomicsDBImport

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    Gökalp Çelik

    Hi HemaRajan

    PoN in Mutect2 is not used as a germline source but a source to exclude sequencing artifacts from Mutect2 calls. If you wish to generate a new germline source for yourself you need to genotype that imported calls and use it as your germline resource file instead of PoN. Mutect2 cannot consume an ungenotyped import. However we highly recommend using our germline resource suggestion as well. You may be able to combine those sites with gnomad-af-only resource for germline to remove possible germline calls from your Mutect2 calls. 

    Regards. 

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