Metadata-Version: 2.1
Name: vanqc
Version: 0.1.0
Summary: Variant Annotator and QC Checker for Human Genome Sequencing
Home-page: https://github.com/dceoy/vanqc.git
Author: Daichi Narushima
Author-email: dnarsil+github@gmail.com
License: UNKNOWN
Description: vanqc
        =====
        
        Variant Annotator and QC Checker for Human Genome Sequencing
        
        [![wercker status](https://app.wercker.com/status/97b0f087b3e5a0a6409aa399611a07bc/s/main "wercker status")](https://app.wercker.com/project/byKey/97b0f087b3e5a0a6409aa399611a07bc)
        ![Upload Python Package](https://github.com/dceoy/vanqc/workflows/Upload%20Python%20Package/badge.svg)
        
        Installation
        ------------
        
        ```sh
        $ pip install -U https://github.com/dceoy/vanqc/archive/main.tar.gz
        ```
        
        Dependent commands:
        
        - `pigz`
        - `bgzip`
        - `tabix`
        - `bcftools` (and `plot-vcfstats`)
        - `java`
        - `snpEff` (`java -jar snpEff.jar`)
        - `gatk`
        - `vep`
        
        Docker image
        ------------
        
        Pull the image from [Docker Hub](https://hub.docker.com/r/dceoy/vanqc/).
        
        ```sh
        $ docker image pull dceoy/vanqc
        ```
        
        Usage
        -----
        
        - Normalize VCF files using Bcftools
        
          ```sh
          $ vanqc normalize /path/to/reference.fa /path/to/variants.vcf.gz
          ```
        
        - Annotate variants using SnpEff
        
          ```sh
          $ vanqc download --snpeff --dest-dir=/path/to/resource
          $ vanqc snpeff \
              /path/to/resource/snpeff_data/GRCh38.86
              /path/to/reference.fa \
              /path/to/variants.vcf.gz
          ```
        
        - Annotate variants using GATK Funcotator
        
          ```sh
          $ vanqc download --funcotator --dest-dir=/path/to/resource
          $ vanqc funcotator \
              /path/to/resource/funcotator_dataSources.v1.7.20200521 \
              /path/to/reference.fa \
              /path/to/variants.vcf.gz
          ```
        
        - Annotate variants using Ensembl VEP
        
          ```sh
          $ vanqc download --vep --dest-dir=/path/to/resource
          $ vanqc vep \
              /path/to/resource/vep_cache/homo_sapiens \
              /path/to/reference.fa \
              /path/to/variants.vcf.gz
          ```
        
        - Collect VCF stats using Bcftools
        
          ```sh
          $ vanqc stats /path/to/reference.fa /path/to/variants.vcf.gz
          ```
        
        - Collect variant calling metrics using GATK (Picard)
        
          ```sh
          $ vanqc metrics \
              /path/to/reference.fa \
              /path/to/dbsnp.vcf.gz \
              /path/to/variants.vcf.gz
          ```
        
        Run `vanqc --help` for more information.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
