Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches.

ABSTRACT: Current variant calling (VC) approaches have been designed to leverage populations of long-range haplotypes and were benchmarked using populations of European descent, whereas most genetic diversity is found in non-European such as Africa populations. Working with these genetically diverse populations, VC tools may produce false positive and false negative results, which may produce misleading conclusions in prioritization of mutations, clinical relevancy and actionability of genes. The most prominent question is which tool or pipeline has a high rate of sensitivity and precision when analysing African data with either low or high sequence coverage, given the high genetic diversity and heterogeneity of this data. Here, a total of 100 synthetic Whole Genome Sequencing (WGS) samples, mimicki

SUBMITTER: Alosaimi S 

PROVIDER: S-EPMC8294538 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature