Spectre - Long read CNV caller

Installation

Recommended ways of installation are using pip or conda or pip package:

pip install ont-spectre

(or)

conda install nanoporetech::ont-spectre

Run from sources

Setup a conda environment for Spectre (copy and paste the following commands)

conda create -n spectre python=3.8.5 pip -y
conda activate spectre
pip install -r requirements.txt

How to run

Spectre need as input:

• The result of Mosdepth (directory)
• Reference genome (can be bgzip compressed)
• Window size used in Mosdepth (Make sure the binsize between Mosdepth and Spectre are matching. We suggest a binsize of 1000 base pairs.)
• VCF file containing SNV

INFO: Make sure to include "/" at the end if you are adding directory paths.

spectre CNVCaller \
  --bin-size 1000 \
  --coverage mosdepth/sampleid/ \
  --sample-id sampleid \
  --output-dir sampleid_output_directory_path/ \
  --reference reference.fasta.gz \
  --snv sampleid.vcf.gz