cg-fluffy 0.4.1

NIPT analysis pipeline

FluFFyPipe

NIPT analysis pipeline, using WisecondorX for detecting aneuplodies and large CNVs, AMYCNE for FFY and PREFACE for FF prediction (optional). FluFFYPipe produces a variety of output files, as well as a per batch csv summary.

Run FluFFyPipe

Run NIPT analysis:

fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> analyse

optionally, skip preface:

fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> --skip_preface analyse

All output will be written to the output folder, this output includes:

bam files
wisecondorX output
tiddit coverage summary
Fetal fraction estimation

as well as a summary csv (per batch)

the input folder is a project folder containing one folder per sample, each of these subfolders contain the fastq file(s). The samplesheet contains at least a "sampleID" column, the sampleID should match the subfolders in the input folder. The samplesheet may contain other columns, such as flowcell and index folder: such columns will be printed to the summary csv.

Create a WisecondorX reference

fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> reference

samplesheet should contain atleast a "sampleID" column. All samples in the samplesheet will be used to construct the reference, visit the WisecondorX manual for more information.

Install FluFFyPipe

FluFFyPipe requires python 3, slurm, slurmpy, and singularity, python-coloredlogs.

First clone fluffypipe:

git clone https://github.com/Clinical-Genomics/fluffy

Install fluffy using pip

cd fluffy

pip install -e .

Next download the FluFFyPipe singularity container

 singularity pull --name FluFFyPipe.sif shub://J35P312/FluFFyPipe

copy the example config (found in example_config), and edit the variables. You will need to download/create the following files:

Reference fasta (indexed using bwa)

WisecondorX reference files (created using the --mkref mode)

PREFACE model file (optional)

blacklist bed file (used by wisecondorX)

FluFFyPipe singularity collection (singularity pull --name FluFFyPipe.sif shub://J35P312/FluFFyPipe)