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

GenomeSTRiP SVGenotyper not producing genotypes

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    Genevieve Brandt

    Bob Handsaker

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    Bob Handsaker

    The diploid genotypes for CNVs are encoded in the CN / CNQ fields, analogous to GT and GQ. CN is the diploid copy number estimate and CNQ is the quality. There is also CNF which is a fractional "point estimate" of the copy number from read depth alone. And CNL gives the likelihood of each copy number class (starting from zero).

     

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