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1000genomescomp

confront

O CONFRONT é um conferidor automático para o cálculo das unidades monitoras e da dose no ponto de cálculo provenientes do sistema de planejamento XiO implementado em R. Como resultado final, o programa resulta um arquivo PDF com diversos parâmetros físicos extraídos do arquivo source do XiO e fatores das tabelas de comissionamento.

depthvariation

Scripst used in the article

mahalanobisdist

Mahalanobis distance between two groups

mosaicsm

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

polygenic_inheritance

Implementation of AI models to identify a polygenic profile for infantile epileptic encephalopathies

sequencingdepth

For a better interpretation of variants, evidence-based databases, such as ClinVar, compile data on the presumed relationships between variants and phenotypes. In this study, we aimed to analyze the pattern of sequencing depth in variants from whole exome sequencing data in the 1000 Genomes project phase 3, focusing on the variants present in the ClinVar database that were predicted to affect protein-coding regions. We demonstrate that the distribution of the sequencing depth varies across different sequencing centers (pair-wise comparison, p<0.001). Most importantly, we found that the distribution pattern of sequencing depth is specific to each facility, making it possible to correctly assign 96.9% of the samples to their sequencing center. Thus, indicating the presence of a systematic bias, related to the methods used in the different facilities, which generates significant variations in breadth and depth in whole exome sequencing data in clinically relevant regions. Our results show that methodological differences, leading to significant heterogeneity in sequencing depth may potentially influence the accuracy of genetic diagnosis. Furthermore, our findings highlight how it is still challenging to integrate results from different sequencing centers, which may also have an impact on genomic research.

varcalling

variantfiltering

wes

Whole Exome Sequencing Workflow