A survey of tools for variant analysis of next-generation genome sequencing data
S Pabinger, A Dander, M Fischer… - Briefings in …, 2014 - academic.oup.com
Recent advances in genome sequencing technologies provide unprecedented opportunities
to characterize individual genomic landscapes and identify mutations relevant for diagnosis …
to characterize individual genomic landscapes and identify mutations relevant for diagnosis …
[HTML][HTML] An analytical framework for optimizing variant discovery from personal genomes
The standardization and performance testing of analysis tools is a prerequisite to
widespread adoption of genome-wide sequencing, particularly in the clinic. However …
widespread adoption of genome-wide sequencing, particularly in the clinic. However …
[HTML][HTML] SeqMule: automated pipeline for analysis of human exome/genome sequencing data
Next-generation sequencing (NGS) technology has greatly helped us identify disease-
contributory variants for Mendelian diseases. However, users are often faced with issues …
contributory variants for Mendelian diseases. However, users are often faced with issues …
An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data
The analysis of next-generation sequencing data is computationally and statistically
challenging because of the massive volume of data and imperfect data quality. We present …
challenging because of the massive volume of data and imperfect data quality. We present …
Using VarScan 2 for germline variant calling and somatic mutation detection
DC Koboldt, DE Larson… - Current protocols in …, 2013 - Wiley Online Library
The identification of small sequence variants remains a challenging but critical step in the
analysis of next‐generation sequencing data. Our variant‐calling tool, VarScan 2, employs …
analysis of next‐generation sequencing data. Our variant‐calling tool, VarScan 2, employs …
[HTML][HTML] Detection of genomic structural variants from next-generation sequencing data
Structural variants are genomic rearrangements larger than 50 bp accounting for around 1%
of the variation among human genomes. They impact on phenotypic diversity and play a role …
of the variation among human genomes. They impact on phenotypic diversity and play a role …
[HTML][HTML] An integrative variant analysis suite for whole exome next-generation sequencing data
Background Whole exome capture sequencing allows researchers to cost-effectively
sequence the coding regions of the genome. Although the exome capture sequencing …
sequence the coding regions of the genome. Although the exome capture sequencing …
A practical guide to filtering and prioritizing genetic variants
MJ Sefid Dashti, J Gamieldien - Biotechniques, 2017 - Taylor & Francis
Next-generation sequencing (NGS) of whole genomes and exomes is a powerful tool in
biomedical research and clinical diagnostics. However, the vast amount of data produced by …
biomedical research and clinical diagnostics. However, the vast amount of data produced by …
[HTML][HTML] Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
Whole-genome sequencing (WGS) is a fundamental technology for research to advance
precision medicine, but the limited availability of portable and user-friendly workflows for …
precision medicine, but the limited availability of portable and user-friendly workflows for …
[HTML][HTML] Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress
The pace of exome and genome sequencing is accelerating, with the identification of many
new disease-causing mutations in research settings, and it is likely that whole exome or …
new disease-causing mutations in research settings, and it is likely that whole exome or …