Mutect2 -- GATK Somatic Short Variant Caller

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

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Tools and workflows for accessing, querying, and analyzing data from the 1000 Genomes Project (1KGP) — the largest public catalog of human genetic variation with whole-genome sequences from 3,202 indi

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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-

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hifiasm — fast haplotype-resolved de novo assembler for PacBio HiFi reads, producing phased telomere-to-telomere genome assemblies. Supports HiFi-only, Hi-C integrated, trio-binning, and ultralong ONT

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RTG Tools — Java-based toolkit from Real Time Genomics for haplotype-aware variant call comparison, VCF filtering, statistics, and pedigree analysis. Primary use: vcfeval for benchmarking variant call

1 shared topic • 2 shared operations