Peter J. Freeman

icon indicating a website link https://www.research.manchester.ac.uk/portal/peter.causey-freeman.html

icon company @openvar icon location The University of Manchester icon location Head developer at VariantValidator Lecturer in Healthcare Sciences (Genomics Bioinformatics) at the University of Manchester

Results 7 comments of Peter J. Freeman

Question about HGVS representation for termination retention

Of course Reece, that makers total sense. The RefSeq Protein reference sequence records do not display the Ter (*). Hence the reference is most certainly '' I agree that certainly...

In-frame del at the end of a transcript throws Index Error

Hi Reece and Paige, I have been taking a look at this error. Sorry if you have moved on, but it’s particularly interesting. Other than giving a warning, I’m not...

In-frame del at the end of a transcript throws Index Error

Great. Happy to help.

Optionally raise exception for variants within ambiguous indel alignment regions

Hi Reece, I'm interested in this proposal. Please can I request that any exception raised will take the form of a warning rather than an error which will prevent mapping....

FLT3 Large Insertion Generating Incorrect HGVS_P

Hi Angie, Asp586Ter would be correct. Ser585_Asp586insTer does not make sense. If you think about this biologically, once you terminate translation following Ser585, the codon for Asp586 would not be...

Consider handling IVS coordinates

Hi Reece and Hannes, Interesting discussion. There are several major issues regarding support for IVS that have not been touched on yet. 1. There is no consensus for numbering Exons,...

Handle transcripts with unaligned regions within exons

I would also agree that it is not necessarily a good idea to support partial alignments. I think the mapping from g. to c. in these instances are better derived...