NanoMethPhase

Phase long reads and CpG methylations from Oxford Nanopore Technologies.

Installation

Using pypi repository

pip install nanomethphase

Using conda

TBD

Creating a dedicated conda environment

Environment file available in the git repository

git clone https://jmgarant@svn.bcgsc.ca/bitbucket/scm/~vakbari/nanomethphase.git
cd nanomethphase
conda env create -f ens/environment.yaml

Quickstart

If you have your methylation call data and phased vcf file you can get the haplotype methylome via:

1- Processing and indexing methylation call file

nanomethphase methyl_call_processor -mc MethylationCall.tsv -t 20 | sort -k1,1 -k2,2n -k3,3n | bgzip > MethylationCall.bed.gz && tabix -p bed MethylationCall.bed.gz

2- Getting haplotype methylome:

nanomethphase phase -mc MethylationCall.bed.gz -o Test_methylome -of bam,methylcall,bam2bis -b sorted.bam -r hg38.fa -v Phased.vcf -t 64

You can select 3 output options:

bam: output phased bam files
methylcall: output phased methylation call and frequency files
bam2bis: output mock whole-genome bisulfite converted bam files

Full Tutorial

In order to get the phased methylome you also need the following third-party software:
Nanopolish : To call CpG methylation.
Clair or other variant callers: To call variants for your sample. Alternatively, you might already have variant calling data for example from Illumina sequencing.
WhatsHap: To phase single nucleotide variants.

Methylation Calling

1- indexing fastq file and fast5 files:
NOTE: Fastqs must be merged to a single file
nanopolish index -d /path/to/fast5s_directory/.fastq

2- Methylation calling for CpG from each read:
nanopolish call-methylation -t <number of threads> -q cpg -r /path/to/fastq_fromstep-1/fastq.fastq -b /path/to/sorted_and_indexed/bam.bam -g /path/to/reference.fa > /path/to/MethylationCall.tsv

Phasing