I have been going through this problem. Is this very common and is there any solution to this error.
Exception in thread "main" java.lang.IllegalStateException: Key . found in VariantContext field INFO at 10:153837 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:173)
at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:112)
at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:224)
at picard.vcf.SortVcf.writeSortedOutput(SortVcf.java:187)
at picard.vcf.SortVcf.doWork(SortVcf.java:105)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)