GATK RNA-Seq Variant Calling in Nextflow

Whole Exome/Whole Genome Sequencing alignment pipeline

Nextflow implementation of the GATK HaplotypeCaller pipeline

Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, realignment around indels, base quality score recalibration (BQSR) and reporting of metrics are optional to maintain flexibility for different use cases.

Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

Workflows for whole-genome/exome sequencing data analysis

Nextflow pipeline for GATK best practices (HaplotypeCaller)

A nextflow pipeline implementing GATK's HaplotypeCaller best practices