Constructing a curl command

[Alistair Ward]

I am trying to use the Mutalyzer API, but cannot figure out how to construct a curl command. I am trying to use the getTranscripts service and am using the command:

curl -s -S -X GET https://mutalyzer.nl/json/getTranscripts?chrom='chr17'&build=hg19&pos=17795221

This results in the error that `build member` must occur at least once. If I switch the order of `build` and `chrom`, then the error changes to `chrom member` must occur at least once. Is there an error in the url construction? I can't find any examples to help.

Thank you for your help,

Director, Research and Science

Eccles Institute of Human Genetics

University of Utah School of Medicine

[J.F.J. Laros]

Dear Alistair Ward,

It seems to be an issue with how you use quotes. Perhaps try the following:

curl -s -S -X GET "https://mutalyzer.nl/json/getTranscripts?chrom=chr17&build=hg19&pos=17795221"

I hope this helps.


With kind regards,
Jeroen.

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[Alistair Ward]

Thanks for getting back to me so quickly! That works. I always get tripped up by these details. Thanks so much for your help,

Alistair Ward, PhD

Co-founder | CEO

Frameshift Genomics Inc.

Director, Research and Science

Eccles Institute of Human Genetics

University of Utah School of Medicine

[Alistair Ward]

I was wondering if there is a way (with Mutalyzer 2 or 3) to get the canonical HGVS starting from the root genomic coordinates. I am always starting with the ref and alt alleles and the coordinates (e.g. chr12, position 102840493, ref=G, alt =A) and want this in HGVS c. and p. notation. Is there a path for this in Mutalyzer?

Thanks again for your help,

Alistair Ward, PhD

Co-founder | CEO

Frameshift Genomics Inc.

Director, Research and Science

Eccles Institute of Human Genetics

University of Utah School of Medicine

[J.F.J. Laros]

Dear Alistair Ward,

If I understand your question correctly, you want to find HGVS coding, RNA
and protein descriptions given a genomic description.

The problem with identifiers like chr12 is that they do not uniquely identify
a reference sequence. I.e., without knowledge about the organism and build,
it is unclear which reference sequence should be used.

When a reference accession number is provided instead (e.g., NC_000012.12),
Mutalyzer 3 will provide an HGVS description for all overlapping transcripts
in the "equivalent descriptions" section [1]. Any of these descriptions can
be selected in order to obtain the RNA and protein effect predictions [2].

I hope this helps.


With kind regards,
Jeroen.

References:
[1] https://v3.mutalyzer.nl/namechecker/NC_000012.12:g.102840493G%3EA
[2] https://v3.mutalyzer.nl/namechecker/NC_000012.12(NM_001354304.2):c.1222C%3ET

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