ArticleMalaria journal2023
An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis.
Article in Malaria journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
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- Clonal haematopoiesis in T-follicular helper cell lymphoma: A prognostic biomarker and early event in lymphoma evolution.British journal of haematology · 2026Article
- Malaria control and the unexpected spread of diagnostic-resistantbioRxiv : the preprint server for biology · 2026Article
- Analysis of physiological and molecular mechanisms of cotton trichome aphid resistance based on SWS-1 mutant.BMC plant biology · 2025Article
- Germline defects of familial haemophagocytic lymphohistiocytosis-Related genes may represent a predisposing factor for mature T- and natural killer-cell lymphoma.British journal of haematology · 2025Article
- Learning-based parallel acceleration for HaplotypeCaller.BMC bioinformatics · 2025Article
- Highly multiplexed molecular inversion probe panel inFrontiers in genetics · 2025Article
- Regular Plasmodium falciparum importation onto Bioko Island, Equatorial Guinea, hampers malaria elimination from the island.PLOS global public health · 2025Article
- A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations.G3 (Bethesda, Md.) · 2024Article
- Long-Read Sequencing andBiology · 2024Article
- Country wide surveillance reveals prevalent artemisinin partial resistance mutations with evidence for multiple origins and expansion of high level sulfadoxine-pyrimethamine resistance mutations in northwest Tanzania.medRxiv : the preprint server for health sciences · 2023Article
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Abstract
backgroundAccurate 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.
methodsControl WGS and accurate PacBio assemblies of 10 laboratory strains were leveraged to optimize parameters that control the heterozygosity, local assembly region size, ploidy, mapping and base quality in both GATK HaplotypeCaller and GenotypeGVCFs. From these controls, a high-quality training dataset was generated to recalibrate the raw variant data.
resultsOn current high-quality samples (read length = 250 bp, insert size = 405-524 bp), the optimized pipeline shows improved sensitivity (86.6 ± 1.7% for SNPs and 82.2 ± 5.9% for indels) compared to the default GATK4 pipeline (77.7 ± 1.3% for SNPs; and 73.1 ± 5.1% for indels, adjusted P < 0.001) and previous variant calling with GATK version 3 (GATK3, 70.3 ± 3.0% for SNPs and 59.7 ± 5.8% for indels, adjusted P < 0.001). Its sensitivity on simulated mixed infection samples (80.8 ± 6.1% for SNPs and 78.3 ± 5.1% for indels) was again improved relative to default GATK4 (68.8 ± 6.0% for SNPs and 38.9 ± 0.7% for indels, adjusted, adjusted P < 0.001). Precision was high and comparable across all pipelines on each type of data tested. The resulting combination of high-quality SNPs and indels increases the resolution of local population population structure detection in sub-Saharan Africa. Finally, increasing ploidy improves the detection of drug resistance mutations and estimation of complexity of infection.
conclusionsOverall, this study provides an optimized falciparum GATK4 pipeline resource for variant calling which should help improve genomic studies of malaria.
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