GRCH37 for Normalizer

[TeodoraTockovska]

Hi! I have used Mutalyzer 2.0 in the past (Position Converter). Could you please add the Assembly feature to Normalizer (Mutalyzer 3.0)? I would like to use Mutalyzer 3 for my tasks but I can't because it lacks the ability to select an assembly (I require GRCh37 assembly).

Since the web application of Mutalyzer 3 searches 1 variant at a time, I assume the best way to submit a list of variants is to use the API. I recommend improving the documentation for the API (specifically adding descriptions for the parameters).

Thanks.

[jfjlaros]

I would like to use Mutalyzer 3 for my tasks but I can't because it lacks the ability to select an assembly

The normalizer accepts the following (unofficial) syntax to select a transcript from an assembly: GRCh37(NM_003002.4):c.274del which leads us to the genomic description NC_000011.9:g.111959695del.

Additionally, the following (also unofficial) syntax can be used to select a chromosome: GRCh37(chr11):g.111959695del which leads us (amongst others) to the transcript description NC_000011.9(NM_003002.4):c.274del.

Is this what you need?

I assume the best way to submit a list of variants is to use the API.

That, or you can use the Batch Processor.

I recommend improving the documentation for the API

I fully agree.

[TeodoraTockovska]

@jfjlaros Thank you for your response, those tips are very helpful!