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

Empty final PON vcf file from 7 samples

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    Genevieve Brandt (she/her)

    Hi Yun Yu, this looks like the same question from your other post. Thanks for reposting so we could get to it after our Out of Office dates

    Let me know if this is a different question that needs to get resolved.

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    David Benjamin

    Yun Yu Only artifacts (and not germline variants) appearing in more than one sample get into the PON.  With only 7 samples it is very possible that no artifact appears more than once.  Unless you have 100+ samples it is best to use one of the PONs in our public google bucket.

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