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

Hard-filtering germline short variants Follow


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    Bhoom Suktitipat

    As of today, some of the images on this post do not show up. I checked the links of these images and they appeared to be in "Google Drive"

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    Chase He

    Hi all, in brief, the recommended thresholds for getting passed variants are QD<2.0, FS>60.0, SOR>3.0, MQ<40.0, MQRankSum < -12.5 and ReadPosRankSum < -8.0. Am I right?

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    Chase He yes this is right.

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