From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

By G. Auwera, Mauricio O. Carneiro, C. Hartl, Ryan Poplin, G. Del Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault and 5 more. Current Protocols in Bioinformatics, 2013

6,636 citations recorded by the source corpus.

This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high‐quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data‐processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key methods involved in variant discovery using the GATK. Curr. Protoc. Bioinform. 43:11.10.1‐11.10.33. © 2013 by John Wiley & Sons, Inc.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/24991f8982dbf109ddc83e053132b61fc5722133

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Citations in the corpus

vcfr: a package to manipulate and visualize variant call format data in R (2017, methodology): “2009) or the GATK’s haplotype caller (McKenna et al. 2010; DePristo et al. 2011; Auwera et al. 2013) have all converged on VCF (Danecek et al.”
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome (2017, result): “Since p21 inhibits, and cyclins D2 and E2 mediate, the G1/S phase transition (Vermeulen et al. 2003), these results are consistent with arrest prior to or slowed progression through S phase seen withDONSON loss in fly and HeLa cells in prior studies (Bandura et al. 2005; Fuchs et al. 2010).”
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients (2018, methodology): “We followed the good-practice guidelines for variant calling withGATK (Van der Auwera et al., 2013).”
MutationalPatterns: comprehensive genome-wide analysis of mutational processes (2016, methodology): “The “surveyed” bases are positions in the genome at which there are enough high-quality reads to reliably call a mutation in that sample, and can be determined using the CallableLoci tool of the Genome Analysis Toolkit (GATK) [28].”