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Position Converter no longer helpful #14
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The position converter from Mutalyzer 2 was not semantically checking nor normalizing the input/output descriptions. Moreover, it was not taking into account the fact that exonic sequences may differ between chromosomal ( To lift (convert) a description over to another reference sequence the Mapper tool from Mutalyzer 3 can be used. In this example Please note that the mapping can be processed also starting from a chromosomal reference to a RefSeq transcript one as here. To help users, we provide the chromosomal descriptions in the "Normalizer" whenever a transcript is used as input and only if the exonic sequences are identical (check this example). When this is not the case, a warning message is being issued, as here. |
How to get geneID and the codant position when we only have genome version and "chr14:g.1524854C>T" ? The position converter for the version 2 of mutalyzer can do this before |
This is true, but the answer Mutalyzer 2 gives ( In Mutalyzer 3, the functionality you need can be found in the Normalizer under the "Equivalent Descriptions" fold. E.g., The only thing that is not supported at the moment is a translation from chromosome number to accession number (e.g., |
Thank you |
Yes, it should work for every build of any organism. GRCh37 and GRCh38 are preloaded though, to speed things up a little. |
Hello, I'm trying to determine how to replicate the behavior of the Mutalyzer v2 Position Converter using the v3 API. In the Mutalyzer v2 API, I routinely used the position converter endpoint to convert from cDNA descriptions, such as the following, to genomic coordinates: NM_000518.4:c.-79A>G In Mutalyzer V2, this input returns the expected result, NC_000011.9:g.5248330T>C, when using the position converter. As I understand it, the new Position Converter endpoint handles positions only, so isn't quite what I'm looking for. I've tried the Mapper using the arguments below, but this input throws errors due to being out of bounds of the reference sequence and a purported mismatch between the transcript and genome sequence, which seems incorrect: Is there a better way to achieve the output I'm looking for, or am I using the v3 API incorrectly? Thank you! |
The description
The only way to describe variants outside of a transcript is to use a genomic reference sequence, e.g., The Normalizer will suggest a "Chromosomal Description" when the following conditions are met:
E.g., for Perhaps Mutalyzer 3 can give some suggestions when one or both of the conditions are not met. In this case, the remark that |
The position converter for the version 2 of mutalyzer was great at distinguishing between transcripts, but now does not seem to provide that function easily. Is it possible to have the previous features?
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