Opened 21 months ago

Last modified 21 months ago

#1229 closed enhancement

Import some variants as annotations — at Version 1

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.26
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

If we find one or more variants in a sample that belongs to a predefined list of "important" variants this information should be imported after the variant calling as an annotation in BASE.

The predefined list of variants should probably be a VCF file with specified chr:pos:ref>alt and some extra information that we can use. We should at least have the GENE name and match that to an annotation type in BASE. For example, if we have a variant:

#CHROM	POS		ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr3	179234297	.	A	G	.	.	GENE=PIK3CA;AA=H1047R

we should import chr3:179234297:A>G to the PIK3CA_Variants annotation (and possibly also the AA tag).

NOTE! The idea is to run this scan/import at the end of the regular variant calling pipeline. To import the same information for existing variant call items, a special script that creates a tab-separated text file (or similar) is needed. The text file can then be imported with the regular annotation importer plug-in.

The list of interesting genes:

  • PIK3CA
  • AKT1
  • SF3B1
  • GATA3
  • ERBB2
  • TP53
  • FOXA1
  • CDH1
  • ESR1

Change History (1)

comment:1 Changed 21 months ago by Nicklas Nordborg

Description: modified (diff)
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