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New ClinVar XML

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@rbutleriii rbutleriii released this 08 Mar 05:47
v1.4.0
bfc699e
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Learn about vigilant mode.

To accommodate the new format of the ClinVar XML, the code has been extensively reworked. While most things could be relocated in this new format, there are some lasting changes.

Fixes:

  • new xml table
  • the output in vcf mode now has no whitespace in the INFO column to be compatible with older VCF format and GATK.
  • ncbi query times and reconnections have been improved

Updates:

  • --long-log now has more thorough reporting of the classification of assertions, for better debugging.
  • CVDS now returns disease IDs to LinkOut. This is due to text descriptions being removed from the new XML format entirely. However, this is easier to parse as an output.
  • Variant types have been implemented in the new xml beyond 'Simple' and 'Haplotype'. These show up in CVVT.
  • Based on the current variant assertions in ClinVar, the assertion weights have been recalibrated.
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