VCF Annotation Tools (VAtools)¶
VAtools is a python package that includes several tools to annotate VCF files with data from other tools.
- vcf-readcount-annotator
A tool that will add the data from bam-readcount files to the VCF sample column. Writes depth, allele counts, and VAFs; optionally also writes detailed per-read quality metrics (mapping quality, base quality, strand counts, and more) as additional FORMAT fields.
- vcf-expression-annotator
A tool that will add the data from several expression tools’ output files to the VCF FORMAT column, on a per-sample basis (use
-sto select the sample for multi-sample VCFs). Directly supports outputs from StringTie, Kallisto, and Cufflinks. There also is acustomoption to annotate with data from any tab-delimited file.- vcf-info-annotator
A general-purpose tool that will add data from a tab-delimited file into VCF INFO fields. Supports mapping multiple TSV columns to multiple INFO fields in a single pass.
- vcf-genotype-annotator
A tool to add a new sample to an existing VCF file or fill in the GT field for an existing sample in a VCF. Fills a need for genotype manipulation in VCFs that don’t contain one, which can cause errors in downstream tools.
- vep-annotation-reporter
A tool to parse the complex VEP-added CSQ field from a VCF and create a tab-delimited (TSV) file of variants and their VEP annotations.
- ref-transcript-mismatch-reporter
A tool to identify variants in a VCF where the reference genome used to align and call variants doesn’t match the Ensembl reference transcript used by VEP for variant consequence annotations.
- transform-split-values
A tool that extracts and manipulates values from existing sample fields and outputs the results to a TSV file.