Tag: FFPE

IDEAFIX – Refinement of Variants in FFPE DNA Sequencing data

IDEAFIX

:: DESCRIPTION

IDEAFIX is a decision tree-based variant refinement tool that filters formaldehyde-induced cytosine deaminations from variant lists obtained from DNA sequencing data from FFPE specimens.

::DEVELOPER

Maitena Tellaetxe Abete

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

IDEAFIX

:: MORE INFORMATION

Citation

Tellaetxe-Abete M, Calvo B, Lawrie C.
Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data.
NAR Genom Bioinform. 2021 Oct 27;3(4):lqab092. doi: 10.1093/nargab/lqab092. PMID: 34729472; PMCID: PMC8557387.

A program suite for Filtering False Somatic Mutations from FFPE Tumor Sequencing data

Filtering False Somatic Mutations from FFPE Tumor Sequencing data

:: DESCRIPTION

This program suite consists of 4 PERL programs made to identify and remove potential false positive somatic variants caused by FFPE (formalin-fixed paraffin-embedded) DNA damage on next-generation sequencing data.

::DEVELOPER

the Division of Genome Information Sciences, UCSD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Perl

:: DOWNLOAD

 program suite

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Aug;40(14):e107. Epub 2012 Apr 6.
Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens.
Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA, Harismendy O, Frazer KA.