Opened 6 months ago

Last modified 6 months ago

#1253 closed defect

Change the name in VCF file created by variant calling — at Initial Version

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.27.2
Component: net.sf.basedb.reggie Keywords:


The current variant calling pipeline gives the parent Library item as the name (-N parameter to VarDict) to use in the VCF file.

This can be a problem for downstream tools since the name is not unique among all VCF files. There are Library items that have been part of more than one pool.

Instead, we should use the name of the Alignment item.

Existing VCF files should be manually fixed (with help of some clever grep/sed/awk/... commands).

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