Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

SelectVariants '-select' example and syntax

KlausNZKlausNZ Posts: 28Member

Just noticed that SelectVariants produces "ERROR MESSAGE: Invalid argument value '>' at position 10" when I use the '-select' parameter with the syntax given in your third example [-select "QD > 10.0"]. I'm using GATK 2.6-5, java/1.7.0_25. It worked well without the whitespace in the expression [-select "QD>10.0"]. Hope that's not just me ;-) Also, does the example miss the line continuation character just before the '-select' option?

No worries, many thanks for the great tool!


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