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Indel variant analysis of short-read sequencing data with Scalpel

Han Fang, Ewa A. Grabowska, Kanika Arora, Vladimir Vacic, Michael C. Zody, Ivan Iossifov, Jason A. O’Rawe, Yiyang Wu, Laura T Jimenez Barron, Julie Rosenbaum, Michael Ronemus, Yoon-ha Lee, Zihua Wang, Gholson J. Lyon, Michael Wigler, Michael C. Schatz, Giuseppe Narzisi
doi: https://doi.org/10.1101/028050
Han Fang
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
3Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
4Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA, 11794
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Ewa A. Grabowska
2New York Genome Center, New York, USA
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Kanika Arora
2New York Genome Center, New York, USA
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Vladimir Vacic
2New York Genome Center, New York, USA
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Michael C. Zody
2New York Genome Center, New York, USA
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Ivan Iossifov
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
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Jason A. O’Rawe
3Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
4Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA, 11794
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Yiyang Wu
3Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
4Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA, 11794
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Laura T Jimenez Barron
3Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
5Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
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Julie Rosenbaum
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
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Michael Ronemus
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
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Yoon-ha Lee
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
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Zihua Wang
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
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Gholson J. Lyon
3Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
4Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA, 11794
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Michael Wigler
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
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Michael C. Schatz
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
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Giuseppe Narzisi
1Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724
2New York Genome Center, New York, USA
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ABSTRACT

As the second most common type of variations in the human genome, insertions and deletions (indels) have been linked to many diseases, but indels of more than a few bases are still challenging to discover from short-read sequencing data. Scalpel (http://scalpel.sourceforge.net) is open-source software for reliable indel detection based on the micro-assembly technique. To date, it has been successfully used to discover mutations in novel candidate genes for autism, and is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole genome and exome sequencing data. We provide detailed instructions for an exemplary family-based de novo study, but we also characterize the other two supported modes of operation for single sample and somatic analysis. Indel normalization, visualization, and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be finished in ~6 hours after read mapping.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 01, 2015.
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Indel variant analysis of short-read sequencing data with Scalpel
Han Fang, Ewa A. Grabowska, Kanika Arora, Vladimir Vacic, Michael C. Zody, Ivan Iossifov, Jason A. O’Rawe, Yiyang Wu, Laura T Jimenez Barron, Julie Rosenbaum, Michael Ronemus, Yoon-ha Lee, Zihua Wang, Gholson J. Lyon, Michael Wigler, Michael C. Schatz, Giuseppe Narzisi
bioRxiv 028050; doi: https://doi.org/10.1101/028050
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Indel variant analysis of short-read sequencing data with Scalpel
Han Fang, Ewa A. Grabowska, Kanika Arora, Vladimir Vacic, Michael C. Zody, Ivan Iossifov, Jason A. O’Rawe, Yiyang Wu, Laura T Jimenez Barron, Julie Rosenbaum, Michael Ronemus, Yoon-ha Lee, Zihua Wang, Gholson J. Lyon, Michael Wigler, Michael C. Schatz, Giuseppe Narzisi
bioRxiv 028050; doi: https://doi.org/10.1101/028050

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