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