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How to do the annotation on unifiedgenotyper?

I used unifiedgenotyper for the variant calling. Here is the result file that I got:
chr1 16919661 . G A 59.74 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=19.91;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:6:87,6,0

The above is the exact the first row in the output file. Should it have the header, like chromosome, position, ref, alt... at the header?
How can I do the variant annotation for this file? I used VariantAnnotator, but I failed. Below is the command:
java -jar $GATK -T VariantAnnotator -R hg38.fa -I sample1_real.bam -V sample1.vcf -o sample1_anno.vcf --resourceAlleleConcordance
And I got the following error message:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file 'Ma_N1.vcf' could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
ERROR Name FeatureType Documentation
ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)
ERROR ------------------------------------------------------------------------------------------

Why it say that this file is not documented within GATK? I generated the file from GATK! Thanks!

Answers

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