Impact of post-alignment processing in variant discovery from whole exome data

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An analytical framework for optimizing variant discovery from personal genomes

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Systematic comparison of variant calling pipelines using gold standard personal exome variants

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Toward better understanding of artifacts in variant calling from high-coverage samples

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Variant detection sensitivity and biases in whole genome and exome sequencing

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Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

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Detailed comparison of two popular variant calling packages for exome and targeted exon studies

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CrossMap: a versatile tool for coordinate conversion between genome assemblies

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Comparing a few SNP calling algorithms using low-coverage sequencing data

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Variant Callers for Next-Generation Sequencing Data: A Comparison Study

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De novo assembly and genotyping of variants using colored de Bruijn graphs

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

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Fast and SNP-tolerant detection of complex variants and splicing in short reads

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Fast and accurate short read alignment with Burrows-Wheeler transform

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SNP detection for massively parallel whole-genome resequencing

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