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Strelka2: Fast and accurate variant calling for clinical sequencing applications

Sangtae Kim, Konrad Scheffler, Aaron L Halpern, Mitchell A Bekritsky, Eunho Noh, Morten Källberg, Xiaoyu Chen, Doruk Beyter, Peter Krusche, Christopher T Saunders
doi: https://doi.org/10.1101/192872
Sangtae Kim
1Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Konrad Scheffler
1Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Aaron L Halpern
1Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Mitchell A Bekritsky
2Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
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Eunho Noh
1Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Morten Källberg
2Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
3Present address: Seven Bridges Genomics, 101 Euston Road, London NW1 2RA, UK
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Xiaoyu Chen
1Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Doruk Beyter
4Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92023, USA
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Peter Krusche
2Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
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Christopher T Saunders
1Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Abstract

We describe Strelka2 (https://github.com/Illumina/strelka), an open-source small variant calling method for clinical germline and somatic sequencing applications. Strelka2 introduces a novel mixture-model based estimation of indel error parameters from each sample, an efficient tiered haplotype modeling strategy and a normal sample contamination model to improve liquid tumor analysis. For both germline and somatic calling, Strelka2 substantially outperforms current leading tools on both variant calling accuracy and compute cost.

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Posted September 23, 2017.
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Strelka2: Fast and accurate variant calling for clinical sequencing applications
Sangtae Kim, Konrad Scheffler, Aaron L Halpern, Mitchell A Bekritsky, Eunho Noh, Morten Källberg, Xiaoyu Chen, Doruk Beyter, Peter Krusche, Christopher T Saunders
bioRxiv 192872; doi: https://doi.org/10.1101/192872
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Strelka2: Fast and accurate variant calling for clinical sequencing applications
Sangtae Kim, Konrad Scheffler, Aaron L Halpern, Mitchell A Bekritsky, Eunho Noh, Morten Källberg, Xiaoyu Chen, Doruk Beyter, Peter Krusche, Christopher T Saunders
bioRxiv 192872; doi: https://doi.org/10.1101/192872

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