For some tasks, writing a script can be overkill. You can do this in a shell:

I am trying to take the first 16 lines of a single file

There's a tool called head which does just that:

$ head -n 16 lines.txt > temp.lines.txt
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and populate those same 16 lines in 34 different (but incrementally named) files

Now use a loop and copy the saved lines to the output files:

$ for i in $(seq 0 33); do cp temp.lines.txt "Annotation_output$i.vcf"
+; done
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And remove the temp file:

$ rm temp.lines.txt
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