Browse Tools

GATK (Genome Analysis Toolkit) — the industry-standard framework for variant discovery in high-throughput sequencing data. Covers the gatk command-line wrapper, Java/JVM tuning, resource bundle manage

GATK HaplotypeCaller — germline short variant caller using localized de novo assembly of haplotypes. Calls SNPs and indels from BAM/CRAM alignment files, producing VCF or gVCF output. Supports single-

Use this skill for GATK-based DNA methylation and bisulfite sequencing workflows including WGBS preprocessing, base quality score recalibration for bisulfite data, duplicate marking of bisulfite reads

GATK VQSR (Variant Quality Score Recalibration) — machine learning-based variant filtering for GATK Best Practices germline pipelines. Trains a Gaussian mixture model on truth/training resource datase

GATK4 — Genome Analysis Toolkit for germline and somatic short variant discovery (SNPs and indels). Industry-standard caller providing HaplotypeCaller for germline, Mutect2 for somatic, plus Base Qual

Mutect2 -- GATK somatic short variant caller for detecting SNVs and indels in tumor samples. Supports tumor-only and tumor-normal paired calling modes with Panel of Normals and germline resource filte

Use when running GATK Mutect2 for somatic SNV and indel detection, low allele frequency (low AF) variant calling, tumor-normal paired somatic mutation analysis, tumor-only somatic calling, panel of no

Use this skill for GATK copy-number variation workflows including germline gCNV cohorts and somatic copy-ratio segmentation from WES or WGS data. Trigger on requests about CollectReadCounts, Determine

Use when working with GATK MarkDuplicates, Picard MarkDuplicates through the GATK wrapper, duplicate marking in BAM or CRAM files, duplicate metrics, or optical duplicate detection in short-read DNA s

GATK ASEReadCounter counts allele-specific expression (ASE) read coverage at heterozygous SNP sites from RNA-seq BAM files. Use for allelic imbalance analysis, ASE quantification, imprinting studies,

This skill compiles a deep skill for funcotator, including finding GitHub repo/API docs, crawling documentation, extracting code examples, EDAM-annotating, adding citations (DOI/PMID), and scoring wit