GLnexus

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

1 shared topic • 2 shared operations

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

1 shared topic • 2 shared operations

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

SnpEff — fast Java-based variant annotation and effect prediction tool that annotates genomic variants (SNPs, indels, MNPs) with gene impact, protein changes, loss-of-function predictions, and HGVS no

1 shared topic • 2 shared operations

SnpSift -- Java-based toolset for filtering, annotating, and manipulating annotated VCF files from SnpEff or other variant callers. Provides expression-based filtering (filter), database annotation wi

1 shared topic • 2 shared operations