Archive | April 2015

Bioinformatics tools for VCF files

Kromozome

With the ever growing abundance of Next Generation Sequencing (NGS) data there continues to be a challenge faced by the research community to not only standardize best practices and analysis methods, but to embrace the foray of open-source tools and file formats. Having been engaged since almost the beginning of this NGS data outburst with Illumina’s read length extending from 30bp to beyond 250bp, for the file format category SAM, BAM and VCF have become well accepted formats to some extent. I say well accepted because a few versions ago CLCbio still reported variants in a csv file format, but maybe I shouldn’t digress.

So in part due to the 1000 Genome Project and Hapmap consortium, formats like VCF are largely accepted as output format as most open-source tools report variants as VCF reports. This has allowed development of tools / parsers to use the file formats as a standard and…

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