Hi friends,
It may be irrelevant to Biostars subject but I would be happy to know about commercial softwares for exome/genome analysis and more important clinical interpretation such as :
Is any body know more about these softwares or list of them ?
Thanks
Also, a side point, since you have already gotten some good answers for lists of commercial software in this space. Commercial isn't necessarily better software. The main advantage of most commercial software is ease-of-use for non-bioinformaticians, and in particular for clinical users. However, I work closely with the local group of Clinical Geneticists and Genetic Counsellors where they are preparing for Clinical Exomes from their lab and they don't want to be personally using this software. They want reports from their lab that they can interpret. They only want to start going through spreadsheets of variants (and ultimately even all this commercial software with fancy GUIs ultimately present data in a columnar format) if there is no good (or a few) clinical candidate variants and it moves on to a more research-oriented case.
Here are my few recommendations:
There are a few which are used as commercial variant analysis tools,
some of it can be found in the link. In the license column it
is described which are for commercial and free. So you can check
for the ones listed as commercial.
You also have the Variant studio from Illumina which can be used and then annotation can be done using ClinVar or HGMD professional etc
There is tool known as SeqReporter which was published 2 years back and claims to be quite significant in addressing clinical variants. I have not tested it but you can take a look.
Alternatively there is another publication referring to Usability
study of clinical exome analysis software. The publication can be
found here. They speak of two softwares Varsifter and KGGSeq
but these are more inclined for using the .vcf format file to
interpret clinical association of variants and prioritizing them.
The most important for clinical context is the association of variants to clinical relevance and prioritizing them. Calling variants can be done with most of the available tools but annotation is the key for diagnostic purposes in clinics and there will play the variant annotation tools a major role.
Hope the answer is useful for you. I will keep updating if I get to know more but would also like others to update if I missed out on some and others have information regarding the same.
We use Cartagenia to interpret variants, you can build a decisiontree once and and throw a vcf in whenever there is data. You can curate the variants that go trough the tree so that they get filtered out in a next iteration.
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+1 for mentioning the caveats and what are the expectations of clinicians while dealing with clinical exomes. Yes I forgot to mention that. It is all about how the results are finally reported and easily interpretable by the clinicians and what leads to more research-oriented case. Thanks for pointing it out.