Variant calling and filtering
VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering.
... alternative variant calling pipelines, and in line with other studies [1, 3–7], we found low concordance between them, especially in the case of ...individual variant callers are complementary ...
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GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data
... accurate variant calling procedure of NGS data including the bioinformatic ...the variant is actually called by all the programs then its support ...the variant is called only by some ...
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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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Alternate-locus aware variant calling in whole genome sequencing
... multiple variant calls against regions of the primary ...of variant calls at positions that we term alignable scaffold-discrepant positions ...and filtering these genomes with our algorithm led to ...
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Validation and assessment of variant calling pipelines for next-generation sequencing
... for variant calling from realigned and recalibrated sequence reads, including UnifiedGenotyper and ...of calling SNPs and insertion/deletion (indels) ...when calling re- gions that are ...
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MASV, a misassembly detection and variant calling pipeline for long reads data
... MASV, a misassembly detection and variant calling pipeline for long reads data. Figure 1.2: Schematic representation of the circular consensus sequence generation through PacBio’s SMRT . The circular DNA ...
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Haplotype Assembly and Small Variant Calling using Emerging Sequencing Technologies
... variants. Filtering SNV calls located near known indels (using the Mills + 1000 Genomes Gold Standard Indels set from the GATK resource bundle [64]), reduced the number of false positives by 34 − 45% for the four ...
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Statistical Methods for Improving Low Frequency Variant Calling in Cancer Genomics
... 2.5.2 Filtering mouse calls from PDX samples One important use case for MAPEX is as a post-variant-calling filter for PDX samples that have been aligned to a human reference ...compared ...
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Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
... by filtering putative SNV based on their average positions in a paired- end ...other variant callers, does not directly test for strand bias or consider read po- sition as a ...
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elPrep: high-performance preparation of sequence alignment/map files for variant calling
... as filtering with the alignment phase ...and variant caller and is open source, so that modifications to these tools are in princi- ple possible; BALSA, while closed source, provides snapshot files, its own ...
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Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads
... The Samovar workflow is shown in Figure 2 and proceeds in six major steps. In step 1, Samovar identifies all genomic sites where there are sufficient data to apply our model. This is done by filtering based on ...
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Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project
... different variant annotations in the set of true positive and false positive sites and established the set of variant annotations and cutoff values used in the ...
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ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets
... In settings where accuracy is a high priority, we rea- soned that an approach that requires agreement between both reads of a read-pair for a given position before the read-pair is allowed to contribute to ...
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A method to reduce ancestry related germline false positives in tumor only somatic variant calling
... a filtering approach is used, the false positive rate is much higher for noncoding variants, as most large scale sequencing projects have fo- cused on coding regions (Additional file 1: Figure ...somatic ...
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Variant filtering, digenic variants, and other challenges in clinical sequencing: a lesson from fibrillinopathies
... First, although WGS is the most comprehensive HTS method offering advantages over targeted sequencing and WES, 25,35 data interpretation remains a challenge. 12 Currently, there is no generally accepted gold standard ...
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Accelerating variant calling
... Local de-novo assembly builds the most likely haplotypes for evaluation. Pair-Hmm evaluation of all reads against all[r] ...
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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
... The core of the CGES package consists of a collection of command line utilities for the harmonization of VCF files, obtained by the means of different variant calling algorithms. Consensus genotypes are ...
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Interactive space-variant image filtering
... The interactive filter steering interfaces developed for controlling the smoothing of shaded images (Chapter 3), and the band-pass filtering over seismic data (Chapter 4), has [r] ...
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A simple data-adaptive probabilistic variant calling model
... The situation for the two diploid genomes A. thaliana and D. melanogaster is different. While both genomes have comparable sizes, the separability of the score distribu- tions varies strongly among these two data sets. ...
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