Detecting genetic variation is one of the main applications of high-throughput sequencing, but is still challenging wherever aligning short reads poses ambiguities. GeneticThesaurus is a method for quick and robust variant detection in low-mappability regions.
(Liu et al., 2013) Variant callers for next-generation sequencing data: a comparison study. PloS one.
(Nielsen et al., 2011) Genotype and SNP calling from next-generation sequencing data. Nature reviews Genetics.
(Altmann et al., 2012) A beginners guide to SNP calling from high-throughput DNA-sequencing data. Human genetics.
(Pabinger et al., 2013) A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics.
(Yi et al., 2014) Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. Nucleic acids research.
(Pirooznia et al., 2014) Validation and assessment of variant calling pipelines for next-generation sequencing. Human genomics.