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The Phantom Variant
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@rbutleriii rbutleriii released this 30 May 04:12
· 14 commits to master since this release
v1.3.1
ab06d1b
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Learn about vigilant mode.

Bugfixes:

  • Move the sleep timer to the end of the batch_local function to make sure it pauses after the first query if that is the only query (<1000 rsids).
  • If any of a few Haplotype Variation IDs are included in the vcf annotation mode, it can create an issue where the other locus in the pair will end up in the annotation table (expected). But this also creates an rsid/alt pair of .|A which then causes all variants with no rsID and an A alt allele to get this clinotator annotation (see VID: 560517, which is rs111033524|A and .|A). Fixed the vcf annotation to prevent rsIDs with . from being annotated, but this then means the Haplotype variant will not be annotated at the .|A locus (which isn't really possible anyways). Keeping track of Haplotype variants requires special attention, and both loci can be retrieved from the vcfmatch field of the tsv table.
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