KRLMM: an adaptive genotype calling method for common and low frequency variants
نویسندگان
چکیده
منابع مشابه
optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants
MOTIVATION Existing microarray genotype-calling algorithms adopt either SNP-by-SNP (SNP-wise) or sample-by-sample (sample-wise) approaches to calling. We have developed a novel genotype-calling algorithm for the Illumina platform, optiCall, that uses both SNP-wise and sample-wise calling to more accurately ascertain genotypes at rare, low-frequency and common variants. RESULTS Using data from...
متن کاملiCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array
MOTIVATION Next-generation genotyping microarrays have been designed with insights from 1000 Genomes Project and whole-exome sequencing studies. These arrays additionally include variants that are typically present at lower frequencies. Determining the genotypes of these variants from hybridization intensities is challenging because there is less support to locate the presence of the minor alle...
متن کاملBRLMM-P: a Genotype Calling Method for the SNP 5.0
Highly accurate and reliable genotype calling is an essential component of any highthroughput SNP genotyping technology. BRLMM, the method of choice for the Mapping 500K product, is effective, but requires the presence of mismatched probes (MM) probes on the array to create “seed” genotypes. We present here a method that only uses perfect-match probes, BRLMM-P. The primary difference between BR...
متن کاملGenotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array
MOTIVATION Due to a genome duplication event in the recent history of salmonids, modern Atlantic salmon (Salmo salar) have a mosaic genome with roughly one-third being tetraploid. This is a complicating factor in genotyping and genetic mapping since polymorphisms within duplicated regions (multisite variants; MSVs) are challenging to call and to assign to the correct paralogue. Standard genotyp...
متن کاملSNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data
We present a statistical framework for estimation and application of sample allele frequency spectra from New-Generation Sequencing (NGS) data. In this method, we first estimate the allele frequency spectrum using maximum likelihood. In contrast to previous methods, the likelihood function is calculated using a dynamic programming algorithm and numerically optimized using analytical derivatives...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2014
ISSN: 1471-2105
DOI: 10.1186/1471-2105-15-158