Best practices for benchmarking germline small-variant calls in human genomes
Sign Up to like & getrecommendations! Published in 2019 at "Nature Biotechnology"
DOI: 10.1038/s41587-019-0054-x
Abstract: Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant-calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part… read more here.
Keywords: variant calling; high confidence; variant calls; variant ... See more keywords
SeqArray—a storage‐efficient high‐performance data format for WGS variant calls
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DOI: 10.1093/bioinformatics/btx145
Abstract: Motivation: Whole‐genome sequencing (WGS) data are being generated at an unprecedented rate. Analysis of WGS data requires a flexible data format to store the different types of DNA variation. Variant call format (VCF) is a… read more here.
Keywords: wgs variant; variant calls; variant; data format ... See more keywords
Prioritisation of structural variant calls in cancer genomes
Sign Up to like & getrecommendations! Published in 2017 at "PeerJ"
DOI: 10.7717/peerj.3166
Abstract: Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe… read more here.
Keywords: prioritisation structural; calls cancer; variant calls; structural variant ... See more keywords