Some complex variants with common prefix - suffix fail the annotation

[rmadupuri]

These variants needs some pre-processing like removing both common prefix and suffixes, adjusting the coordinates etc., before passing to GN. It's a bit tricky in some cases.

Chr	Start Pos	End Pos	Ref Allele	Tumor Allele
5	112175377	112175378	CAAAAG	CAAAAAT
17	7578231	7578232	CAAAT	CAAAAAT
17	7578439	7578440	TTGT	TGCTTGG
5	112175650	112175651	TAAAAAT	TAAAAAAT
20	31022441	31022442	AGGGGGGGGT	AGGGGGGGGGT
22	41574678	41574679	GCCCCCCCA	GCCCCCCCCA
2	48033651	48033652	AAATT	AAATAATT
17	11924243	11924244	GGCGGCAGCGGCAGCGGCAC	GGCGGCAGCGGCAGCGGCAGCGGCAC
6	157100116	157100117	AGGCGGCGGCGGCGGCGGCT	AGGCGGCGGCGGCGGCGGCGGCT
6	157099165	157099166	GTCCTCCTCCTCCTCCTCCTCCG	GTCCTCCTCCTCCTCCTCCTCCTCCG
1	27023007	27023008	AGGCGGCGGCGGCGGCA	AGGCGGCGGCGGCGGCGGCGGCA
7	55248999	55249000	TGGCCAGCGTGGAC	TGGCCAGCGTGGCCAGCGTGGAT
7	55242460	55242461	ATCAAGGAATTAAGAGAAGCA	ATCAAAGGAATTAAGAGAAGCA
7	55249015	55249016	CCCC	CCCAACCCCT
7	151874147	151874148	CTTTTTTTTTG	CTTTTTTTTTTG
17	7577091	7577092	GCCG	GCCCCG
16	67660601	67660602	GATT	GATATT
7	55248999	55249000	TGGCCAGCGTGGAC	TGGCCAGCCGTGGAC
19	1221313	1221314	GCCCCCCG	GCCCCCCTG
17	7578467	7578475	GACGCGGGT	GACGCGGG
7	55242465	55242482	CAAGGAATTAAGAGAAGC	CAA
9	1393967398	1393967410	GTCCTCGCCGAGG	GCCCTC
X	66766357	66766356	GGCGGCGGCGGCGGCGGCGGC	-
17	7577541	7577540	TTCATGCCGCCCATGCAGGAA	-