SelectVariants - Error
Posted in Ask the GATK team | Last updated on 2013-11-13 17:06:24


Comments (4)

Hi,

I am trying to subset a few samples from a VCF using the following command

java -Xmx8g -jar GenomeAnalysisTK-2.6-4-g3e5ff60/GenomeAnalysisTK.jar -T SelectVariants -R Homo_sapiens_assembly19.fasta -V Input.vcf -sf samples.txt-o Out.vcf

Getting the error

ERROR MESSAGE: Key Indel_FS,Indel_QD found in VariantContext field FILTER at 1:985458 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.

I checked the Input.vcf and can find that the following lines exists in the VCF

##FILTER=<ID=Indel_FS,Description="FS>200.0">
##FILTER=<ID=Indel_QD,Description="QD<2.0">

Not sure why the error ?

Any help much appreciated.. Many Thanks, Tinu


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