Filtering de novo indels in parent-offspring trios

Genotype calling and haplotyping in parent-offspring trios.

Emerging sequencing technologies allow common and rare variants to be systematically assayed across the human genome in many individuals. In order to improve variant detection and genotype calling, raw sequence data are typically examined across many individuals. Here, we describe a method for genotype calling in settings where sequence data are available for unrelated individuals and parent-of...

Detection of de novo copy number alterations in case-parent trios using the R package MinimumDistance

For the analysis of case-parent trio genotyping arrays, copy number variants (CNV) appearing in the offspring that differ from the parental copy numbers are often of interest (de novo CNV). This package defines a statistic, referred to as the minimum distance, for identifying de novo copy number alterations in the offspring. We smooth the minimum distance using the circular binary segmentation ...

A Bayesian framework for de novo mutation calling in parents-offspring trios

MOTIVATION Spontaneous (de novo) mutations play an important role in the disease etiology of a range of complex diseases. Identifying de novo mutations (DNMs) in sporadic cases provides an effective strategy to find genes or genomic regions implicated in the genetics of disease. High-throughput next-generation sequencing enables genome- or exome-wide detection of DNMs by sequencing parents-prob...

Finding de novo copy number variants in case-parent trios for oral clefts

trio-sga: facilitating de novo assembly of highly heterozygous genomes with parent-child trios

Motivation: Most DNA sequence in diploid organisms is found in two copies, one contributed by the mother and the other by the father. The high density of differences between the maternally and paternally contributed sequences (heterozygous sites) in some organisms makes de novo genome assembly very challenging, even for algorithms specifically designed to deal with these cases. Therefore, vario...