Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

The main aim of this little project is to compare the European allele frequencies of the 1k genomes project with the gnomad frequencies.

Convert SV VCFs to BED, a wrapper for bcftools query

Code final year dynamic genome visualizer project.

A pipeline for filtering annotated variant call format files

Repository for scripts used to estimate guppy (Poecilia reticulata) mutation rate.

Automated variant annotation pipeline, and curated OMIM and ClinVar SNV datasets, developed by Martina Debnath.

a tool for quickly getting the correct bcftools command

Data Access Agreement fulfillment pipeline: VCF genotype extraction, sample list validation, SQL metadata parsing, and IN-clause query generation for biobank releases

bioinformatics

End-to-end NGS variant calling and gene annotation pipeline using Linux bioinformatics tools.