add example usage to docs

Author: kcotto

docs/index.md

@@ -27,6 +27,34 @@ make
 regtools --help
 ```
 
+If one wishes to test their installation, we include test data under `test_data`. 
+
+Here's an example command using that data along with the example output.
+
+```sh
+regtools cis-splice-effects identify -s RF -e 10 -i 10 test_data/HCC1395_chr22.vcf.gz test_data/HCC1395_tumor.bam test_data/chr22_with_ERCC92.fa test_data/chr22_with_ERCC92.gtf
+
+Variant 22	42129188	42129189	-1
+Variant region is 22:42128784-42130813
+
+chrom	start	end	name	score	strand	splice_site	acceptors_skipped	exons_skipped	donors_skipped	anchor	known_donor	known_acceptor	known_junction	gene_names	gene_ids	transcripts	variant_info
+position = 22:42125408-42125409
+position = 22:42130565-42130566
+22	42125407	42130567	JUNC00000001	4	+	GT-AG	0	0	0	D	1	0	0	NDUFA6-AS1	ENSG00000237037	ENST00000439129	22:42129188-42129189
+position = 22:42128881-42128882
+position = 22:42129670-42129671
+22	42128880	42129672	JUNC00000002	3	+	GT-AG	0	0	0	N	0	0	0	NA	NA	NA	22:42129188-42129189
+position = 22:42128944-42128945
+position = 22:42129031-42129032
+22	42128943	42129033	JUNC00000003	4	-	GT-GG	1	0	0	D	1	0	0	CYP2D6	ENSG00000100197	ENST00000360608,ENST00000389970,ENST00000488442	22:42129188-42129189
+position = 22:42129783-42129784
+position = 22:42143453-42143454
+22	42129782	42143455	JUNC00000004	2	+	GC-AG	9	8	9	N	0	0	0	NA	NA	NA	22:42129188-42129189
+position = 22:42130224-42130225
+position = 22:42130565-42130566
+22	42130223	42130567	JUNC00000005	2	+	GT-AG	0	0	0	N	0	0	0	NA	NA	NA	22:42129188-42129189
+```
+
 For information about the individual RegTools commands, please see [the Commands page](commands/commands.md)
 
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