“VCF annotation” with the NHLBI GO Exome Sequencing Project (JAX-WS) by Pierre Lindenbaum.
From the post:
The NHLBI Exome Sequencing Project (ESP) has released a web service to query their data. “The goal of the NHLBI GO Exome Sequencing Project (ESP) is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders.“.
In the current post, I’ll show how I’ve used this web service to annotate a VCF file with this information.
The web service provided by the ESP is based on the SOAP protocol.
Important news/post for several reasons:
First and foremost, “for the potential to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders.”
Second, thanks to Pierre, we have a fully worked example of how to perform the annotation.
Last but not least, the NHLBI Exome Sequencing Project (ESP) did not try to go it alone for the annotations. It did what it does well and then offered the data up for other to use/extend it, hopefully to be used/extended by others.
I can’t count the number of projects of varying sorts that I have seen that tried to do every feature, every annotation, every imaging, every transcription, on their own. All of which resulted in being less than they could have been with greater openness.
I am not suggesting that vendors need to give away data. Vendors for the most part support all of us. It is disingenuous to pretend otherwise. So vendors making money means we get to pay our bills, buy books and computers, etc.
What I am suggesting is that vendors, researches and users need to work towards (yelling at each other doesn’t count) towards commercially viable solutions that enable greater collaboration with regard to research and data.
Otherwise we will have impoverished data sets that are never quite what they could be and vendors will be many many times over the real cost of developing data. Those two conditions don’t benefit anyone. “You, me, them.” (Blues Brothers) 😉