This filtering step is necessary due to the fact that there may be tens of thousands of false variants present in the variant call sets.Ĭurrent state-of-the-art filtering methods include Frequency 25, Hard-Filter 20, VQSR 26, GARFIELD 27, VEF 28, ForestQC 29 and so on, which employ different strategies in addressing the filtering task. Variant filters are then applied to eliminate false variants made by the variant caller. Variant callers, such as GATK HaplotypeCaller 19, 20, Mutect2 21, Varscan2 22, 23, and DeepVariant 24, are utilized to identify the positions and the genotypes of the genomic variants. The procedure includes at least two main software elements: the variant caller and the variant filter. One prominent application with clinical relevance is the utilization of WGS data and bioinformatics tools to identify single nucleotide variants (SNV) and insertion and deletion (INDEL) variants in a single individual genome. Whole-genome sequencing (WGS) has been widely used in diagnosing genetic disorders in the pediatrics 1– 4, exploring causative relations with tumor progression 5– 7, studying genetic variation underlying pharmaceutical response 8– 10, performing genome-level comparative analysis 11, 12, assessing gene expression 13– 15, and providing clinical insights and instructions 16– 18.
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