dceoy/vanqc repository overview

⁠vanqc

Variant Annotator and QC Checker for Human Genome Sequencing

⁠Installation

$ pip install -U vanqc

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
  

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• 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
  

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• 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
  

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• 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
  

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• Collect VCF stats using Bcftools

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

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• Collect variant calling metrics using GATK (Picard)

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

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Run vanqc --help for more information.