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(a), Distributions of the Y82C and I97M variants across all gnomAD populations.
We report 240 pathogenic variants across all cases, including 84 of 86 known from previous diagnostic testing (98% sensitivity).
Polymorphisms were called using the GATK pipeline41, which considers indel realignment and base quality score recalibration, and calls variants across all samples simultaneously through the HaplotypeCaller program in GATK41.
Whole-exome sequencing (WES) studies allow a more comprehensive analysis of rare coding variants across all genes of the genome and will contribute to a better understanding of the underlying disease mechanisms.
Due to these limitations, it is unlikely that the goal of completely characterizing the human transcriptome, including all transcript variants across all tissues, disease states, and developmental stages, will be accomplished by full-length cDNA sequencing alone.
(C) Boxplot of BC variants across all samples.
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Because ethical concerns usually prevent the sharing of genotype and phenotype information between collaborators, genetic consortia tend to analyze summary statistic data; that is, association results for each variant across all participating studies [ 61].
ANNOVAR reports the most severe consequence for a variant across all transcripts present at that position in the genome, so with more transcripts available when using ENSEMBL there is an elevated chance of finding a more severe consequence for one of the ENSEMBL transcripts.
Additionally, the total number of variants present across all samples and the number of variants unique to only one sample is given.
Of the 22 behavioral variants recorded across all sites, on average 57% occurred in the social domain, 19% in food-related domains and 24% in other domains.
Genotype samples (GenotypeGVCFs): gVCFs used to call variants jointly across all samples, exomes, or genomes: a serial stage.
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