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

Mutect2 Follow

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    Hi, I run mutect with two parameters `--genotype-germline-sites true  --genotype-pon-sites true ` to preserve germline sites, but in the output vcf file, the genotypes(GT) of the normal samples are all 0/0. Why?


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