nanomethphase 0.0

Phase long reads from Oxford Nanopore Technologies based on their methylated profile.

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://[e-mail]/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