Exomiser
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exomiser
Homozygosity mapping
Peter knows Tommasso Pippucci pretty well (see https://www.ncbi.nlm.nih.gov/pubmed/?term=pippucci+t+homozygosity) so could implement his algorithms within Exomiser and just limit the phenotype search within the autozgosity intervals.
Hi! I would love to start work on this -- can we define a good interface that we can code to? Do you are Jules have time to work on this? Are there some samples to test?
Lets talk on Friday in the roadmap meeting! I have one set of cases from Exeter to test against at least.
On Tue, Jul 11, 2017 at 12:47 AM, Peter Robinson [email protected] wrote:
Hi! I would love to start work on this -- can we define a good interface that we can code to? Do you are Jules have time to work on this? Are there some samples to test?
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Hey all,
I'm currently looking for a homozygosity mapper/Loss of Heterozygosity caller and was wondering if this is still something you hope to incorporate into Exomiser? I really love the program quality and the fast support you guys offer. I was looking into H3M2 for a loh caller (https://sourceforge.net/projects/h3m2/), but the program is incomplete with very poor documentation. If you guys are looking to incorporate this into Exomiser, that would be fantastic. If it's not something that is high priority, do you have any recommendations for an LOH caller for Exomes?
Thank you for your time, Kyle
Coming back to this I wonder if it would make sense to have some auxilliary apps for Exomiser that would perform homozygosity mapping and our IBD2 mapping. The output of these programs could be a file that would list the intervals that passed the filter and thus would interdigitate well with the current Exomiser architecture. Probably this is not something we can do in the very short term.
With Exomiser becoming more of a comprehensive tool (future CNV analysis, homozygosity mapping, etc.), I think that would make the most sense. From what I've experienced, it would make sense to couple LOH and CNV in an auxiliary app.