vanqc

Variant Annotator and QC Checker for Human Genome Sequencing

Installation

$ 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.

$ docker image pull dceoy/vanqc

Usage

• Normalize VCF files using Bcftools

  $ vanqc normalize /path/to/reference.fa /path/to/variants.vcf.gz
  

• Annotate variants using SnpEff

  $ 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

  $ 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

  $ 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

  $ vanqc stats /path/to/reference.fa /path/to/variants.vcf.gz
  

• Collect variant calling metrics using GATK (Picard)

  $ vanqc metrics \
      /path/to/reference.fa \
      /path/to/dbsnp.vcf.gz \
      /path/to/variants.vcf.gz
  

Run vanqc --help for more information.