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Article

An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis.

Malaria journal - 7 Jul 2023

Niaré Karamoko, Greenhouse Bryan, Bailey Jeffrey A

Abstract excerpt

BACKGROUND: Accurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here a falciparum variant calling pipeline based on GATK version 4 (GATK4) was optimized and applied to 6626 public Illumina WGS samples. METHODS: Control WGS and accurate PacBio assemblies of 10 laboratory strains were leveraged to optimize parameters that control...

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Identifiers

PMID: 37420214
DOI: 10.1186/s12936-023-04632-0
PMCID: PMC10327343

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026. Manifest publication-graph-cohort-2026-09-07.1.

Source receipt: pubmed, retrieved 7 Sept 2026.

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