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HGVS variant nomenclature checker
https://mutalyzer.nl
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Issue about SNP Converter #482

Closed ionicbond2005 closed 5 years ago

ionicbond2005 commented 5 years ago

Hi,

I am trying to use batch SNP converter. However, when I try to give a list of rsID, the output was just Non existing "my rsID" in the DB or no root element.

I lookup some of my rsID on dbSNP and they are valid

Would you mind fixing this issue?

Thank you batch-job-a8f4acc7-b89d-4027-8968-ffceafcb7435.txt

Attached is the output

jfjlaros commented 5 years ago

Thank you for reporting this.

@mihailefter Apparently the NCBI response changed. The HGVS descriptions are now located in the DOCSUM tag.

mihailefter commented 5 years ago

@ionicbond2005 This issue is now fixed.

ionicbond2005 commented 5 years ago

one question:

If the variant does not has an rsID, can mutalyzer use other information such as chromosome + positon + reference allele + alternate alllele and convert into HGVS nomenclature?

Thank you

On Wed, Aug 21, 2019 at 5:55 AM mihailefter notifications@github.com wrote:

@ionicbond2005 https://github.com/ionicbond2005 This issue is now fixed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/mutalyzer/mutalyzer/issues/482?email_source=notifications&email_token=AB3747AR7Y6ZA5MF3CFM4WDQFUGKXA5CNFSM4ILFTWY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4ZEBTQ#issuecomment-523387086, or mute the thread https://github.com/notifications/unsubscribe-auth/AB3747COHB7MFCERL3ML663QFUGKXANCNFSM4ILFTWYQ .

mihailefter commented 4 years ago

@ionicbond2005 it looks like you have all the ingredients that constitute an HGVS description, so just put them together as a substitution variant ('>), include also the coordinate system (.g), and that's it. If you miss the accession.version of a chromosome, then you can make use of the Position Converter to retrieve it. Pass it next through the Name Checker to see its correctness.

If you are actually interested in VCF to HGVS, then you can make use of Mutalyzer Client.