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

Funcotator maf has different alt allele than vcf for some variants


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    Philipp Hähnel

    Hi Balthasar,

    do you also see an adjacent multi-nucleotide variant TGGC>GGGG in the maf? I think Mutect2 chooses a reducible form of indels in the form of MNV + pure indel, here TGGC>GGGG plus G insertion. Funcotator with VCF output has probably combined those two variants into TGGC>GGGGG.



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