SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples.

ABSTRACT:

Background

Artifact chimeric reads are enriched in next-generation sequencing data generated from formalin-fixed paraffin-embedded (FFPE) samples. Previous work indicated that these reads are characterized by erroneous split-read support that is interpreted as evidence of structural variants. Thus, a large number of false-positive structural variants are detected. To our knowledge, no tool is currently available to specifically call or filter structural variants in FFPE samples. To overcome this gap, we developed 2 R packages: SimFFPE and FilterFFPE.

Results

SimFFPE is a read simulator, specifically designed for next-generation sequencing data from FFPE samples. A mixture of characteristic artifact chimeric reads, as well as normal reads, is generated. FilterFFPE is a filtra

SUBMITTER: Wei L 

PROVIDER: S-EPMC8458033 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature