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.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
Files:
Customer Reviews
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