vanqc 0.1.0

Description:

vanqc 0.1.0

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.