دورية أكاديمية
أعرض في EDS

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

التفاصيل البيبلوغرافية
العنوان: An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis
المؤلفون: Karamoko Niaré, Bryan Greenhouse, Jeffrey A. Bailey
المصدر: Malaria Journal, Vol 22, Iss 1, Pp 1-11 (2023)
بيانات النشر: BMC, 2023.
سنة النشر: 2023
المجموعة: LCC:Arctic medicine. Tropical medicine
LCC:Infectious and parasitic diseases
مصطلحات موضوعية: Arctic medicine. Tropical medicine, RC955-962, Infectious and parasitic diseases, RC109-216
الوصف: Abstract 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 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. Results On 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
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1475-2875
العلاقة: https://doaj.org/toc/1475-2875Test
DOI: 10.1186/s12936-023-04632-0
الوصول الحر: https://doaj.org/article/4ed3bc8ae86f4836a93c9be673f5ace1Test
رقم الانضمام: edsdoj.4ed3bc8ae86f4836a93c9be673f5ace1
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:14752875
DOI:10.1186/s12936-023-04632-0