recipe bioconductor-filterffpe

FFPE Artificial Chimeric Read Filter for NGS data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/FilterFFPE.html

License:

LGPL-3

Recipe:

/bioconductor-filterffpe/meta.yaml

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

Versions:

1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

Depends:

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-doparallel

• r-foreach

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-filterffpe

and update with:

conda update bioconductor-filterffpe

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-filterffpe:<tag>

(see bioconductor-filterffpe/tags for valid values for <tag>)

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