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

Somatic short variant discovery (SNVs + Indels) Follow

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    Linda Do

    Hi! It is not clear how to use the GetPileupSummaries and CalculateContamination in the text above.  Which tool do I use first?  Or are they supposed to be used simultaneously?

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    Tina

    Can this pipeline be used for calling SNVs + Indels on single-cell ATAC-seq or single-cell RNA-seq data? 

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