Variant Annotator and QC Checker for Human Genome Sequencing
Project description
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
(andplot-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.
Project details
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