Alternate Reference Maker

When I run the command:
java -jar '/home/bushra/Downloads/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar' -T FastaAlternateReferenceMaker -R '/home/bushra/Downloads/Brassica/Bra1.27.fa' -o '/home/bushra/Downloads/outputseq.fasta' -V '/home/bushra/Downloads/Brassica/Bra1.27-juncea-B.vcf' on ubuntu I get the following error:

ERROR MESSAGE: VCFHeaderLine: key cannot contain angle brackets

even though the vcf fileheader doesn't contain any angle brackets. when i try validating the vcf file, it gives the same error and I am not able to move forward.

Answers

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