GATK best-practice germline pipeline (CPU)
CPU workflow of BWA alignment, GATK duplicate marking, base recalibration and HaplotypeCaller, with DeepVariant as an alternative caller.
No reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
CPU workflow of BWA alignment, GATK duplicate marking, base recalibration and HaplotypeCaller, with DeepVariant as an alternative caller.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
0 evaluations · 0 results. Different protocols are not a single leaderboard.
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Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
1 source records and release history
- Benchmarking accelerated next-generation sequencing analysis pipelines · Original source · Bioinformatics Advances 5(1):vbaf085, published 2025-05-15; PMC12092081 full-text XML
Technical metadata and extraction receipts
Stable ID: model-execution-20261009-method-gatk-best-practices-cpu
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- CPU-only pipeline
- entity level
- method
- source locator
- Methods and table labels of the cited sources
- missing metadata
- version: reason: inapplicable; note: Family record; versions are on configurations