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

Whole genome Pooled sequnce data analysis


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    Bhanu Gandham

    Hi Tania Zahid


    We do not have a pooled samples variant calling pipeline. We think Mutect2 should work since it takes into account probabilistic fluctuations in the proportional coverage, i.e. not assume that exactly X% of reads come from each of the 100/X samples. We have not tested this on our end so please use at your own discretion. 

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