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FFPolish

Filters Artifacts From Formalin-Fixed Paraffin-Embedded (FFPE) Variants

Installation

Conda Installation

Ensure that you have the conda-forge and bioconda channels in the correct priority order.

conda config --show channels
channels:
  - conda-forge
  - bioconda
  - defaults

If the above command doesn't have the correct output, run:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

To create a new environment named ffpolish with FFPolish installed, run:

conda create -n ffpolish -c matnguyen ffpolish

Activate the environment

source activate ffpolish

And run FFPolish, producing the help output

ffpolish -h

Running FFPolish

Filtering VCF

You can filter artifacts from a VCF using the pre-trained model.

Input Requirements

  • A reference genome in FASTA format
  • A bgzipped VCF file of FFPE variants
  • A BAM file of the FFPE tumour

Command

The available options are:

  • -o/--outdir - the output directory (default: current directory)
  • -p/--prefix - the output prefix (default: basename of the BAM)

FFPolish can be run with the following command and outputs a filtered vcf out_filtered.vcf:

ffpolish filter -o outfolder -p out reference.fa vcf.gz tumour.bam

Retraining Model With New Data

We recommend that if you have ground truth data (paired FFPE and fresh frozen tumours), you should create your own dataset to augment the included training set at least with a partial subset of your data.

Input Requirements

  • A reference genome in FASTA format
  • A bgzipped VCF file of FFPE variants
  • A BAM file of the FFPE tumour
  • A tab-delimited file of true variants
  • Output directory

Tab delimited format:

Column Definition
chr Chromosome
start Start position
end End position
ref Reference allele
alt Alternate allele

Command

The available options are:

  • -p/--prefix - the output prefix (default: basename of the BAM)
ffpolish extract -p out reference.fa vcf.gz tumour.bam labels.tsv outdir