Bioinformatics tools for VCF files

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 [...]


Exomes vs Genomes (re-visited)

The paper by Lupski et al in Genome Medicine provides fuel to the perpetual debate of Whole Exome Sequencing (WES) vs Whole Genome Sequencing (WGS). It takes me down the memory lane to my own presentation "Genomes or Exomes: evaluation of cost, time and coverage" at Beyond the Genome 2011 conference. (If you would like [...]

Mitochondrial Gold Rush

Mitochondrial genomes can be extracted from Whole Exome Sequencing (WES) data as outlined by this paper in Nature methods by Ernesto Picardi & Graziano Pesole. Tools like Mito Seek are now available that gather mitochondrial read sequences from NGS data and perform high throughput sequence analysis. Availability of mitochondrial genomes is important as genomic variation in mitochondria has [...]

#ASHG2013 Platform and Poster abstract tag-clouds

With more than 6000 scientists (genetics, bioinformatics, clinicians, statistics, genetic counselor...) and more than 200 companies at Boston for this year's American Society for Human Genetics conference, there is a lot of great science to catch up on. Very quickly, I just pulled out the selected platform talk abstracts, and the poster abstracts (too many [...]

R Line Plots – the easiest fastest plot ever

What you need: Data R Eager Bioinformatician For data I used a file with 7 columns where the first column was a counter and the other columns (2-7) had different values that I would like to compare across using a line plot to visualize the variation in my data points Serves: As many data points [...]

How recent are rare variants?

The Department of Genome Sciences at the University of Washington in Seattle, in a multi-institutional effort sequenced 15,336 genes for the NHLBI sponsored ESP project from a total of 6515 individuals of European American and African American descent.To identify approaches for disease-gene discovery, its important to understand evolutionary history of homosapiens and identify the age [...]

Journal Club: Indels in 179 genomes (1000genome data)

The origin, evolution and functional impact of short insertion-deletion variants identified in 179 human genomes Genome Research Finally there is a comprehensive analysis on indels, and of course it is the Next Generation Sequencing data that is driving it. I have my concerns with the biases of NGS technology and analysis along with ensuing false-positives [...]