Metadata-Version: 2.1
Name: nanomethphase
Version: 0.0
Summary: Phase long reads from Oxford Nanopore Technologies based on their methylated profile.
Home-page: UNKNOWN
Author: Vahid Akbari
Author-email: vakbari@bcgsc.ca
License: UNKNOWN
Project-URL: GitHub, https://github.com/vahidAK/NanoMethPhase
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](https://svn.bcgsc.ca/bitbucket/users/vakbari/repos/nanomethphase/browse)
        
        ```
        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](https://github.com/jts/nanopolish) : To call CpG methylation.  
        [Clair](https://github.com/HKU-BAL/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](https://github.com/whatshap/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
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3.7
Description-Content-Type: text/markdown
