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

pooled experiment means

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    Genevieve Brandt (she/her)

    lizhichao can you clarify your question further with more details?

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    Genevieve Brandt (she/her)

    Hi lizhichao,

    A pooled experiment is different from joint calling. It means when you combined the DNA of many individuals and sequenced them together. The DNA is not separated by sample. With joint calling, even though the data is analyzed together, the samples were sequenced and can be analyzed separately.

    Best,

    Genevieve

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    lizhichao

    Thanks, your repsponse is the exact answer to what  i concerned. So I don't have to manually set the --ploidy when I run joint-calling with different samples input.

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    Genevieve Brandt (she/her)

    Yes, that's correct! 

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