Force diff/vimdiff to adjust line comparison

I'm comparing a couple files for differences using vimdiff. In this case, one file has 11 lines of comments describing the file whereas the other has no comment lines. I was surprised that vimdiff (rather, the underlying 'diff' ) did not accurately assign which lines to compare, so every line is different. In this case, line 12 from the first file should be compared to line 1 from the second.

Question: Is there a way to adjust which lines vimdiff (or the underlying diff) compares (e.g., shift down by 12), without modifying the files?

Really appreciate your help.

Here are initial lines from the files:

File 1 (includes comments)

# This table shows the intersection of dark by MAPQ regions by a gene annotation gff3, showing where dark by MAPQ regions fall within gene body # chrom : Chromosome of dark by MAPQ region # region_start : start position of dark by MAPQ region within gene-body element # region_end : end position of dark by MAPQ region within gene-body element # gene_body_id : ID of gene body element that contains this dark by MAPQ region # region_type : genebody element type (e.g. exon, intron, UTR, etc.) # biotype : GENCODE biotype of gene that contains this dark by MAPQ reigon # gene_body_chrom : Chromosome of the genebody element # gene_body_start : start position of the genebody element # gene_body_end : end position of the genebody element #chrom start end gene_body_id region_type biotype gene_body_chrom gene_body_start gene_body_end 1 11869 12227 DDX11L1_1 exon transcribed_unprocessed_pseudogene 1 11869 12227 1 12228 12611 DDX11L1_intron_1 intron transcribed_unprocessed_pseudogene 1 12228 12611 1 12612 12721 DDX11L1_2 exon transcribed_unprocessed_pseudogene 1 12612 12721 1 12722 12751 DDX11L1_intron_2 intron transcribed_unprocessed_pseudogene 1 12722 12973 1 12861 12973 DDX11L1_intron_2 intron transcribed_unprocessed_pseudogene 1 12722 12973 1 13191 13219 DDX11L1_intron_3 intron transcribed_unprocessed_pseudogene 1 13053 13219 

File 2 (does not include comments)

chr1 11869 12227 DDX11L1_1 exon transcribed_unprocessed_pseudogene chr1 11869 12227 chr1 12228 12611 DDX11L1_intron_1 intron transcribed_unprocessed_pseudogene chr1 12228 12611 chr1 12612 12721 DDX11L1_2 exon transcribed_unprocessed_pseudogene chr1 12612 12721 chr1 12722 12752 DDX11L1_intron_2 intron transcribed_unprocessed_pseudogene chr1 12722 12973 chr1 12861 12973 DDX11L1_intron_2 intron transcribed_unprocessed_pseudogene chr1 12722 12973 chr1 13191 13219 DDX11L1_intron_3 intron transcribed_unprocessed_pseudogene chr1 13053 13219 

VimDiff result