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

Question

[esproff]

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?

Answer 1

[Pierre Lindenbaum]

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>

[GenoMax]

hgvs variations are in this file.

[esproff]

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

[esproff]

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