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

Pre-adapter artifacts (in hybrid selection) - Bait bias Follow

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    Thanks for the glossary entry.

    Perhaps you a conflating two different concepts here? I am not sure that reference bias (the tendency to miss alignments or report incorrect alignments for reads containing non-reference alleles 10.1186/s13059-020-02229-3, 10.1186/s13059-020-02160-7) is the same thing as bait bias as suggested above? Reference bias also occurs in the absence of any hybridization enrichment steps... I am not sure the point you are trying to make with the example you give...

    all the best, thanks

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