elPrep

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

2 shared topics • 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

2 shared topics • 2 shared operations

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

2 shared topics • 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

2 shared topics • 2 shared operations

Strelka2 — fast and accurate small variant caller for germline and somatic analysis. Detects SNVs and indels (up to ~49 bp) from mapped paired-end sequencing reads with tiered haplotype modeling, adap

2 shared topics • 2 shared operations