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 [...]

Advertisements

Venn Diagrams Simplified

Not a week goes by without me having to compare multiple lists to evaluate overlap. Re-analyzing any data and comparing that with previously computed data, comparing results from multiple tools or multiple samples. Sometimes the unix commands diff, paste and join come handy, but most times am looking for some additional information. Almost always, am [...]

The common story of rare variants..

NGS comes to the aid of researchers to find answers for herited complex traits and diseases, paving a path towards the ‘personalized medicine era’. Whole-exome sequencing (WES) has been deployed for identifying rare variants associated with complex diseases and is providing a philip for further research and insight. Common variants that were identified through Genome [...]

Clinical Findings from Sequencing keep flowing…

Just a glance at GenomeWeb's "In Print: Clinical Sequencing Papers of Note of the Last Two Weeks" is enough to show how hard it is to keep up with the sequencing revolution. Of the 37 publications mentioned here, 15 talk about whole-exome sequencing (WES) (and two amplicon sequencing and three whole-genome seq) identifying the causal [...]

The New Genomes of 2012

From the first large genome (goat's genome) to be sequenced and assembled de novo using whole-genome mapping technology, published almost a week ago to around 1000 rice genomes sequenced at 1x coverage: there's a lot that has happened at the Whole Genome Sequencing level. Roche/454 is still being used and so is Sanger, not everyone [...]

MAQ SNPfilter

MAQ is this very vesatile and popular tool for mapping of short read data (Solexa, SOLiD). This is a very curious case. I used MAQ to call SNPs on a Solexa data of 6.5 million 36bp reads. I used maq map .. followed by maq.pl SNPfilter using all defaults. Interestingly, I trimmed the 1st two [...]

BLAT

Blat is a useful algorithm in the Bioinformatics world dominated with blast! Its even named Blast Like Alignment Tool. I was recently fiddling with blat alignment on human data, and realized how fast and easy blat can be. Working on next-gen data, Solexa reads is what I had. One of the cool things was, use [...]