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Where to find the file Variant.Alternate designations on the ClinVar FTP server?

I'm looking for the Variant.Alternate designations file on the ClinVar FTP server. Supposedly this file exists per this document found here: https://www.ncbi.nlm.nih.gov/projects/clinvar/ClinVarDataDictionary.pdf.

I've searched through what I believe to be the entirety of ClinVar's FTP server and haven't been able to find this file. Basically I'm trying to scrape all alternative variant names for a subset of the mutations listed on ClinVar (these names for a specific mutation are listed next to the Other names bullet on the mutation's associated page).

Can anyone help me find this file?

gene variant clinvar
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by esproff • esproff

1 answer

you'd better try to parse the XML file. Everything is here:

curl -s "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2017-04.xml.gz" | gunzip  -c |grep -i 'Type="HGVS"'
          <Attribute Type="HGVS">NM_000018.2:c.1182+1G>A</Attribute>
          <Attribute Type="HGVS">NC_000001.11:g.231351570_231351573del</Attribute>
          <Attribute Type="HGVS">NM_032018.5:c.717_718+2delAGGT</Attribute>
          <Attribute Type="HGVS">NM_017777.3:c.1408-35_1408-7del</Attribute>
          <Attribute Type="HGVS">NM_018136.4:c.1152_1153delAG</Attribute>
          <Attribute Type="HGVS">NM_018136.4:c.1152_1153del</Attribute>
          <Attribute Type="HGVS">NM_014251.2:c.851_854del</Attribute>
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written by Pierre Lindenbaum Pierre Lindenbaum

I wasn't able to find the alternative names in that file unfortunately.

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written by esproff • esproff

So the code you've given me just lists all mutations correct? How would I go about extracting the alternative mutation names?

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written by esproff • esproff

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