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Variant detection and genotype calling using Genome Analysis Tool Kit (GATK)

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posted on 20.11.2020, 05:13 by Amanda Chamberlain, Christy J. Vander Jagt, Fazel Almasi
In this lecture, we will describe the variant (SNP and INDEL) detection pipeline used by the 1000 bull genomes project. The pipeline closely follows the Genome Analysis Tool Kit (GATK, Broad Institute) best practises. Tools that are used to process raw sequence reads for individuals and align them to the genome will be described in detail, including a Base Quality Sequence Recalibration step to detect and correct for patterns of systematic errors in the base quality scores. Also, the tools used to detect variants and call genotypes across all samples and then filter variants using a recalibration against known variants, resulting in a dataset that balances precision and sensitivity.

Funding

Intellectual Climate Fund

History

First created date

04/11/2020

School

  • School of Life Sciences

Publication Date

20/11/2020

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n/a

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The Author reserves all moral rights over the deposited text and must be credited if any re-use occurs. Documents deposited in OPAL are the Open Access versions of outputs published elsewhere. Changes resulting from the publishing process may therefore not be reflected in this document. The final published version may be obtained via the publisher’s DOI. Please note that additional copyright and access restrictions may apply to the published version.

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