bcftools

Learning the Variant Call Format

Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

BioC++ Input/Output library

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

A modern, high-performance, composable genomics foundation for .NET, with strongly typed genomic models, sequences, streaming I/O, indexing, algorithms, and pipelines. Includes the original 12-week Genomics for Software Engineers course and hands-on learning materials.

A Nextflow variant normalization pipeline based on vt and bcftools

A collection of scripts for filtering annotated variant call format files

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

Curated cheatsheet of high-efficiency Linux, AWK, SAMtools, BCFtools, SeqKit, and Python one-liners for daily genomic data manipulation.

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

Nextflow resequencing pipeline with bwa-mem and freebayes

Merge in parallel, speeding up bcftools merge

GATK4 germline variant calling (Nextflow DSL2): BWA-MEM -> MarkDuplicates -> BQSR -> HaplotypeCaller -> hard-filter, benchmarked against a GIAB truth set (precision/recall/F1).

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

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

Comprehensive NGS analysis including whole genome sequencing, RNA-Seq, variant calling, and visualization using bioinformatics pipelines

Germline short-variant calling Nextflow DSL2 pipeline: BWA-MEM2 + bcftools mpileup/call + MultiQC

Bioinformatics pipelines and analysis scripts for trio-based detection of Mendelian inheritance errors and de novo mutations in F1 prairie × mojave rattlesnake hybrid offspring.

End-to-end E. coli Whole Genome Sequencing (WGS) pipeline using FastQC, Trimmomatic, BWA, SAMtools and BCFtools from raw FASTQ to variant calling.