What question did this study set out to answer?

To present an optimized, scalable computational protocol using cgpPindel for accurately identifying somatically acquired insertions and deletions in cancer sequencing data.

December 1, 2015Current Protocols in BioinformaticsOpen Access

cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing

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To present an optimized, scalable computational protocol using cgpPindel for accurately identifying somatically acquired insertions and deletions in cancer sequencing data.
Adapted the Pindel algorithm to detect somatic insertions and deletions by comparing paired-end sequence data from cancer samples against matched reference controls.
Implemented post-hoc filtering mechanisms to systematically remove false-positive indel predictions.
Developed execution procedures for both single-instance runs and distributed, large-scale compute farm environments.
The tool generates refined, high-quality somatic indel call sets suitable for rigorous downstream genomic investigations by filtering out sequencing artifacts.
The protocol successfully scales from single-sample workflows to high-throughput compute cluster architectures.

Implication

Software pipeline demonstrates accurate detection of somatic insertions and deletions in cancer genomes, highlighting scalable workflows for paired-end sequencing data.

Abstract

cgpPindel is a modified version of Pindel that is optimized for detecting somatic insertions and deletions (indels) in cancer genomes and other samples compared to a reference control. Post-hoc filters remove false positive calls, resulting in a high-quality dataset for downstream analysis. This unit provides concise instructions for both a simple 'one-shot' execution of cgpPindel and a more detailed approach suitable for large-scale compute farms.

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Cite This Study

Raine et al. (2015) studied this question.

synapsesocial.com/papers/6a197d6bf9a68600c7d997e1 https://doi.org/10.1002/0471250953.bi1507s52

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Implication

Software pipeline demonstrates accurate detection of somatic insertions and deletions in cancer genomes, highlighting scalable workflows for paired-end sequencing data.

cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing

Key Points

Implication

Abstract

Discussion

Cite This Study

cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing

Key Points

Implication

Abstract

Discussion

Cite This Study

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