FilterFFPE

The software tool 'FilterFFPE' addresses the challenge of artifact chimeric reads in next-generation sequencing data from formalin-fixed paraffin-embedded (FFPE) samples. These chimeric reads can lead to false-positive structural variant calls. The tool consists of two R packages: SimFFPE, a read simulator for FFPE samples, and FilterFFPE, a filtration algorithm designed to remove artifact chimeric reads while preserving genuine chimeric reads.

Topic

Sequencing;Structural variation;Sample collections

Detail

  • Operation: Variant calling;Variant filtering;Standardisation and normalisation

  • Software interface: Library

  • Language: R

  • License: GNU Lesser General Public License v3.0

  • Cost: Free

  • Version name: 1.12.0

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Lanying Wei lanying.wei@uni-muenster.de

  • Collection: -

  • Maturity: Stable

Publications

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Download and documentation

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