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
Not sure why the error ?
Any help much appreciated.. Many Thanks, Tinu