- recipe bioconductor-filterffpe
FFPE Artificial Chimeric Read Filter for NGS data
This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.
- package bioconductor-filterffpe¶
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-rsamtools:
- depends bioconductor-s4vectors:
- depends r-base:
- depends r-doparallel:
- depends r-foreach:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-filterffpe and update with:: mamba update bioconductor-filterffpe
To create a new environment, run:
mamba create --name myenvname bioconductor-filterffpe
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-filterffpe:<tag> (see `bioconductor-filterffpe/tags`_ for valid values for ``<tag>``)