Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads
نویسندگان
چکیده
منابع مشابه
A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to en...
متن کاملBest practices for evaluating single nucleotide variant calling methods for microbial genomics
Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing platforms requires careful attention to detail for robust results. Thus far, much of the scientific Communit's focus for use in bacterial genomics...
متن کاملAssessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals
MOTIVATION Whole-genome sequencing (WGS) is now routinely used for the detection and identification of genetic variants, particularly single nucleotide polymorphisms (SNPs) in humans, and this has provided valuable new insights into human diversity, population histories and genetic association studies of traits and diseases. However, this relies on accurate detection and genotyping calling of t...
متن کاملComparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample
Next-generation sequencings platforms coupled with advanced bioinformatic tools enable re-sequencing of the human genome at high-speed and large cost savings. We compare sequencing platforms from Roche/454(GS FLX), Illumina/HiSeq (HiSeq 2000), and Life Technologies/SOLiD (SOLiD 3 ECC) for their ability to identify single nucleotide substitutions in whole genome sequences from the same human sam...
متن کاملA statistical variant calling approach from pedigree information and local haplotyping with phase informative reads
MOTIVATION Variant calling from genome-wide sequencing data is essential for the analysis of disease-causing mutations and elucidation of disease mechanisms. However, variant calling in low coverage regions is difficult due to sequence read errors and mapping errors. Hence, variant calling approaches that are robust to low coverage data are demanded. RESULTS We propose a new variant calling a...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: iScience
سال: 2019
ISSN: 2589-0042
DOI: 10.1016/j.isci.2019.05.037