Single nucleotide and indel variant calling
Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads
... mosaic variant call to be ‘‘validated’’ if (1) the corresponding WES tumor sample had at least 50 aligned reads at the locus with at least 4 reads supporting the mosaic allele, and (2) the mosaic variant ...
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CiteSeerX — Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
... break Swap Curr and Prev; return Match Fermi corrects errors in two phases. In the first phase, it collects all 23 mer occurring 3 or more times using a top-down traversal over the trie represented by the FMD-index. For ...
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Hadoop-based solutions for variant calling and variant analysis
... ant calling pipelines implemented in Halvade, researchers interested in the analysis of VCF files benefit a lot from an interactive and visual environment, unimpeded by scalability issues that may arise from ...
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Structural variant calling: the long and the short of it
... Of note, NanoSV reports only breakpoints (BND) which again makes the interpretation of the SVs type difficult. Overall, long-read mapping-based methods for SV calling often show a better performance than ...
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CoVaCS : a consensus variant calling system
... Custom targeted resequencing panels can be analyzed by simply uploading a file in bed format, specifying the co- ordinates of targeted regions. Pipelines for joint- (jsp) and single-sample (ssp) variant ...
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Performance evaluation of indel calling tools using real short-read data
... any variant is computed by comparing the likelihood of the data given all haplo- types and the likelihood given only those haplotypes that do not include a particular ...called indel with the default ...
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Systematic comparative analysis of single nucleotide variant detection methods from single cell RNA sequencing data
... and variant allele ...low variant ratios could also re- duce the ...the variant de- tection ...in variant calling for scRNA-seq data, which should be noticed in future benchmarking ...
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Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses
... common variant analysis, the recessive and co-dominant models yielded some high odds ratio estimates but also wide con- fidence intervals (as expected, as these are the models with relatively low ...rare ...
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Indel and single nucleotide variations of zeins generate unique 2D-zein patterns and molecular markers useful in maize (Zea mays) genotyping
... In this study, we investigated the inter- and intra-genomic sequence variation of alpha-zein genes and their poly- peptide expression in different maize genotypes, i.e. inbreds and a set of Lombardy open pollinated ...
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Introduction to Galaxy Platform for NGS Variant Calling Pipeline
... aligned nucleotide, which can ultimately be brought together by measuring differences between the most likely and the second most likely genotypes/observation frequency as a measure of confidence with the highest ...
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Assessment of genomic variant calling methods through simulations
... SNPs occurring at consecutive bases are sometimes denoted as multi-nucleotide poly- morphism or MNP. Due to grouping into codons, the effect on a SNP depends on its context. If the SNP changes an AGA codon into an ...
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Algorithm for automatic genotype calling of single nucleotide polymorphisms using the full course of TaqMan real-time data
... are all located in the lower left-hand corner of each graph. Similar results were observed for the remaining 7 SNPs (Supplementary Figure 2). In BCGA, samples are classified according to the differ- ences in their ...
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Genome wide joint analysis of single nucleotide variant sets and gene expression for hypertension and related phenotypes
... The whole-genome joint analysis of 3 phenotypes was completed in 80 min using a single core of i7 4700 CPU with 8 GB memory. Table 1 summarizes the top genes from the analysis, which were selected based on the ...
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Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.
... INTRODUCTION Copy number variants (CNVs) are duplications, insertions or deletions of chromosomal segments that are 1 kb (1,2). Multiple experimental techniques can detect CNVs, including bacterial artificial chromosome ...
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Assessing the pathogenicity of insertion and deletion variants with the Variant Effect Scoring Tool (VEST-Indel)
... importantly, pathogenic classification from VEST-indel and DDIG- in is complementary rather than entirely overlapping, hence the increased sensitivity relative to either method alone. As expected, however, the ...
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Alternate-locus aware variant calling in whole genome sequencing
... alternate loci. This offers many opportunities to the genomics and bioinformatics communities to adapt anal- ysis procedures to a more sophisticated model of the human genome, but it also presents substantial technical ...
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Validation and assessment of variant calling pipelines for next-generation sequencing
... multi-stage pipeline for processing the exome data on these subjects and then examined the accuracy of calls derived from different implementations of the pipeline by validation with Sanger sequencing of a total of 700 ...
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Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine
... clude single nucleotide variants (SNVs), short insertions/de- letions (indels), or fusion ...EGFR single base mutation (L858R) in exon 21 and in-frame deletions (ranging from 12 to 18 bases) in exon ...
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Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
... resulting variant calls, we kept only biallelic SNPs and selected heterozygous ...excluded variant calls with quality score below ...and calling variants as described ...
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Genetic Analysis Workshop 18 single nucleotide variant prioritization based on protein impact, sequence conservation, and gene annotation
... rare variant association ...(GAW18) single-nucleotide variants; we focused on variants detected by whole genome sequencing, specifically on the high-quality subset presented in the genotype ...the ...
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