Metadata-Version: 2.1
Name: mutract
Version: 1.1
Summary: Extracting single cell variants from bam file
Home-page: https://github.com/singleron-RD/mutract
Author: zhouyiqi
Author-email: zhouyiqi@singleronbio.com
License: UNKNOWN
Description: # Mutract
        Mutract is a tool for extracting single cell variants from bam file. If vcf file is not provided, it will perform variant calling at single cell level.
        
        ## Requirements
        - python > 3.6
        - GATK
        - samtools
        
        ## Installation
        `pip install mutract`
        
        GATK and samtools can be installed via conda.
        
        ## Usage
        ```
        mutract \
        --bam bam_file \
        --barcodes cell_barcodes_file \
        --fasta reference_fasta_file \
        --vcf vcf_file \
        --sample sample_name \
        --outdir output_directory \
        --thread 8 \
        --gene_file gene_file \
        ```
        
        - Required Arguments
        
        `bam` Input CeleScope BAM file. If gene_file is specified, the BAM must have the 'GN' tag.
        
        `barcodes` Cell barcodes file, one barcode per line.
        
        `fasta` Reference genome fasta, must be indexed.
        
        `sample` Sample name.
        
        - Optional Arguments
        
        `vcf` VCF file. If vcf file is not provided, mutract will perform variant calling at single cell level and use these variants as input vcf.
        
        `outdir` Output directory, default='./'.
        
        `thread` The number of threads to use,  default=1.
        
        `gene_file` Gene list file, one gene symbol per line. Only variants of these genes are reported.
        
        ## Output
        
        `{sample}_VID.tsv` A unique numeric ID is assigned for each variant.
        
        `{sample}_CID.tsv` A unique numeric ID is assigned for each cell.
        
        `{sample}_variant_count.tsv`  Reference and variant supporting reads/UMIs count.
        
        `{sample}_support.mtx` Support matrix, only high quality bases are considered.   
        0 : no reads/UMIs cover the position.  
        1 : all reads/UMIs at the position support the ref allele.  
        2 : all reads/UMIs at the position support the alt allele.  
        3 : one or more reads/UMIs support both the alt and the ref allele.  
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
