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

How to recover a mutation from secondary alignment

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    David Benjamin

    Laurent MANCHON The command line given above filters secondary and supplementary alignments (it turns on the corresponding read filters, which is also the default behavior).  The program log most likely reports no reads filtered in this way because they fail the mapping quality filter first.

    However, even if you disable these filters you will end up with a lot of mapping errors and double-counted variants.  Simply running Mutect2 would not produce sensible output.

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    David Benjamin

    By the way, to turn off a read filter, use the --disable-read-filter argument.

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