decon2vcf 1.0.1

Convert Decon Output to VCF format.

DeconToVCF

Introduction

This is a tool to convert multiple DeCon .txt [1] file outputs generated in pipelines into a single genomic VCF format file that can then be used for annotation software and further analysis tools.

Download the directory:

git clone [e-mail]:AWGL/DeconToVCF.git

Requirements

The python script needs to be run with arguments

• -d = path to decon output directory. The directory should be the folder containing all of the decon outputs "raw_data".
• -p = path to ped file.
• -o = path and filename of choice for the output. The programme will not create directories that do not already exist.

To run the programme

• create environment from .yaml file and activate

pip install decon2vcf

• run programme with arguments

python DeconToVCF -d <path-to-decon-output-directory> -p <path-to-ped-file> -o <path/filename-for-output-file>

eg:

python DeconToVCF -d /data/runid/post-processing/results/cnv_svs/raw_data/ -p post-processing/results/ped/file.ped -o post-processing/results/DeconToVCF_output.vcf

References

[1] https://www.imm.ox.ac.uk/research/research-groups/lunter-group/lunter-group/decon-detection-of-exon-copy-number