Examples

Below are some examples of the kinds of transcript that ExonViz can create.

SDHD

Visualise two variants in the SDHD gene

exonviz --transcript "NM_003002.4:r.[274g>u;300del]" --exonnumber > SDHD.svg

NF1

Visualise NF1, setting the width of the figure to the size of the largest exon

exonviz --transcript "ENST00000358273.9" --noncoding --width 3600 --height 75 > NF1-202.svg

Schematic representation of DMD

Create a schematic visualisation of the DMD gene. Since this gene is very large, we will first export the exons to TSV format, and then modify each exon to have the same size.

# Write the exons in TSV format to dmd.tsv
exonviz --transcript DMD --exonnumber --dump-exons DMD-schematic.tsv

# Next, modify each exon to be 30 bp in your favorite text editor
# Don't forget to also update the size of the coding region for each exon
# (see the table below)

# Finally, draw the exons from the TSV file
exonviz --exon-tsv DMD-schematic.tsv --width 750 --gap 0 > DMD-schematic.svg

TSV file for schematic representation of DMD
size	name	color	coding_start	coding_end	start_phase	end_phase
30	1	#4C72B7	0	30	0	1
30	2	#4C72B7	0	30	1	0
30	3	#4C72B7	0	30	0	0
30	4	#4C72B7	0	30	0	0
30	5	#4C72B7	0	30	0	0
30	6	#4C72B7	0	30	0	2
30	7	#4C72B7	0	30	2	1
30	8	#4C72B7	0	30	1	0
30	9	#4C72B7	0	30	0	0
30	10	#4C72B7	0	30	0	0
30	11	#4C72B7	0	30	0	2
30	12	#4C72B7	0	30	2	0
30	13	#4C72B7	0	30	0	0
30	14	#4C72B7	0	30	0	0
30	15	#4C72B7	0	30	0	0
30	16	#4C72B7	0	30	0	0
30	17	#4C72B7	0	30	0	2
30	18	#4C72B7	0	30	2	0
30	19	#4C72B7	0	30	0	1
30	20	#4C72B7	0	30	1	0
30	21	#4C72B7	0	30	0	1
30	22	#4C72B7	0	30	1	0
30	23	#4C72B7	0	30	0	0
30	24	#4C72B7	0	30	0	0
30	25	#4C72B7	0	30	0	0
30	26	#4C72B7	0	30	0	0
30	27	#4C72B7	0	30	0	0
30	28	#4C72B7	0	30	0	0
30	29	#4C72B7	0	30	0	0
30	30	#4C72B7	0	30	0	0
30	31	#4C72B7	0	30	0	0
30	32	#4C72B7	0	30	0	0
30	33	#4C72B7	0	30	0	0
30	34	#4C72B7	0	30	0	0
30	35	#4C72B7	0	30	0	0
30	36	#4C72B7	0	30	0	0
30	37	#4C72B7	0	30	0	0
30	38	#4C72B7	0	30	0	0
30	39	#4C72B7	0	30	0	0
30	40	#4C72B7	0	30	0	0
30	41	#4C72B7	0	30	0	0
30	42	#4C72B7	0	30	0	0
30	43	#4C72B7	0	30	0	2
30	44	#4C72B7	0	30	2	0
30	45	#4C72B7	0	30	0	2
30	46	#4C72B7	0	30	2	0
30	47	#4C72B7	0	30	0	0
30	48	#4C72B7	0	30	0	0
30	49	#4C72B7	0	30	0	0
30	50	#4C72B7	0	30	0	1
30	51	#4C72B7	0	30	1	0
30	52	#4C72B7	0	30	0	1
30	53	#4C72B7	0	30	1	0
30	54	#4C72B7	0	30	0	2
30	55	#4C72B7	0	30	2	0
30	56	#4C72B7	0	30	0	2
30	57	#4C72B7	0	30	2	0
30	58	#4C72B7	0	30	0	1
30	59	#4C72B7	0	30	1	0
30	60	#4C72B7	0	30	0	0
30	61	#4C72B7	0	30	0	1
30	62	#4C72B7	0	30	1	2
30	63	#4C72B7	0	30	2	1
30	64	#4C72B7	0	30	1	1
30	65	#4C72B7	0	30	1	2
30	66	#4C72B7	0	30	2	1
30	67	#4C72B7	0	30	1	0
30	68	#4C72B7	0	30	0	2
30	69	#4C72B7	0	30	2	0
30	70	#4C72B7	0	30	0	2
30	71	#4C72B7	0	30	2	2
30	72	#4C72B7	0	30	2	2
30	73	#4C72B7	0	30	2	2
30	74	#4C72B7	0	30	2	2
30	75	#4C72B7	0	30	2	0
30	76	#4C72B7	0	30	0	1
30	77	#4C72B7	0	30	1	1
30	78	#4C72B7	0	30	1	0
30	79	#4C72B7	0	30	0	0

DM20 and PLP1

The PLP1 gene has two main isoforms, namely PLP1 (ENST00000621218.5) and DM20 (ENST00000619236.1). DM20 is the shorter form of the protein, missing the last 35 amino acids from the third exon. Either isoform can be drawn by ExonViz directly. In the literature, the third exon is often divided in two parts. The first part, termed 3A is present in each isoform, while the second part, termed 3B, is missing from DM20 (for example, Shy et al., 2016). The figure and associated TSV file are shown below, note that exon 3 has been split into two parts, 3A and 3B.

exonviz --exon-tsv PLP1-DM20.tsv --scale 1.3 --gap 0 > PLP1-DM20.svg

TSV file for PLP1 and DM20
size	name	color	coding_start	coding_end	start_phase	end_phase
4	1	#4C72B7	0	4	0	1
187	2	#4C72B7	0	187	1	2
157	3A	#4C72B7	0	157	2	0
105	3B	#4C72B7	0	105	0	0
169	4	#4C72B7	0	169	0	1
74	5	#4C72B7	0	74	1	0
66	6	#4C72B7	0	66	0	0
72	7	#4C72B7	0	72	0	0

NDUFAF6 cryptic exon

Catania et al., 2018 describe a deep intronic variant in NDUFAF6 which leads to the inclusion of a 124nt cryptic exon.

exonviz --exon-tsv NDUFAF6.tsv  > NDUFAF6.svg

TSV file for NDUFAF6 cryptic exon
size	name	color	coding_start	coding_end	start_phase	end_phase
197	1	#4C72B7	0	197	0	2
100	2	#4C72B7	0	100	2	0
123	3	#4C72B7	0	123	0	0
124	cryptic exon	darkred	0	0	0	0
57	4	#4C72B7	0	57	0	0
103	5	#4C72B7	0	103	0	1
134	6	#4C72B7	0	134	1	0
102	7	#4C72B7	0	102	0	0
57	8	#4C72B7	0	57	0	0
129	9	#4C72B7	0	129	0	0

CYLD

CYLD is a tumor suppressor gene, which has a clear mutational hotspot in exon 16. In the figure below, all ClinVar variants for CYLD transcript NM_001378743.1 have been visualized using ExonViz. This figure uses colors that are clearly distinguishable for color blind people, thanks to this useful website.

How to create the figure

Generating a figure such as this is fairly involved, since it requires gathering all variants for a given transcript, and then modifying them so they are displayed per category.

Gather the variants

The following should be repeated for every variant category of interest, we will use the category Likely Pathogenic as an example. At the time of writing, this gives the following HGVS description:

NM_001378743.1(CYLD):c.[454_455del;1111del;2040dup;2282_2283del;2616del;2723dup].

Note that intronic variants such as 1684+2T>C should not be included, since they are outside of the exons.

Visit ClinVar and Download all variants in Tabular (text) format.
Open the file in a spreadsheet program, and order all variants using the Germline consequence option.
Create a compound HGVS description for all variants in a category, for example Likely Pathogenic.

Export the variants

Use ExonViz to export the exons and variants to TSV files to maninpulate

exonviz --dump-variants likely-pathogenic.tsv --transcript "NM_001378743.1:c.[454_455del;1111del;2040dup;2282_2283del;2616del;2723dup]" --scale 1.2 > /dev/null

Raw likely pathogenic variants for CYLD
exon	position	name	color
3	453	c.454_455del	#BA1C30
8	89	c.1111del	#DB6917
13	90	c.2040dup	#EBCE2B
16	40	c.2282_2283del	#702C8C
18	146	c.2616del	#C0BD7F
19	36	c.2723dup	#BA1C30

Update the variants

Open the likely-pathogenic.tsv file in a spreadsheet program, and update the name column to contain (Likely) Pathognic, and the color option to #882255 for each variant.

Updated likely pathogenic variants for CYLD
exon	position	name	color
3	453	(Likely) Pathogenic	#882255
8	89	(Likely) Pathogenic	#882255
13	90	(Likely) Pathogenic	#882255
16	40	(Likely) Pathogenic	#882255
18	146	(Likely) Pathogenic	#882255
19	36	(Likely) Pathogenic	#882255

Draw the figure with ExonViz

Repeat the above steps for each category from ClinVar you are interested in. When you are satisfied with the variants, you can merge all categories into a single file. You can then draw CYLD from the tsv files you have created. ExonViz will recognise that there are multiple variants with the same name and color, and will only include each combination in the legend only once.

exonviz --width 747 --exon-tsv CYLD-exons.tsv --variant-tsv CYLD-variants.tsv --scale 1.2 --variantshape bar > CYLD.svg

Exons for CYLD
size	name	color	coding_start	coding_end	start_phase	end_phase
0	1	#88CCEE	0	0	0	0
0	2	#88CCEE	0	0	0	0
504	3	#88CCEE	0	504	0	0
303	4	#88CCEE	0	303	0	0
106	5	#88CCEE	0	106	0	1
9	6	#88CCEE	0	9	1	1
99	7	#88CCEE	0	99	1	1
117	8	#88CCEE	0	117	1	1
380	9	#88CCEE	0	380	1	0
166	10	#88CCEE	0	166	0	1
142	11	#88CCEE	0	142	1	2
123	12	#88CCEE	0	123	2	2
92	13	#88CCEE	0	92	2	1
67	14	#88CCEE	0	67	1	2
133	15	#88CCEE	0	133	2	0
109	16	#88CCEE	0	109	0	1
119	17	#88CCEE	0	119	1	0
217	18	#88CCEE	0	217	0	1
185	19	#88CCEE	0	185	1	0

Variants for CYLD
exon	position	name	color
3	86	(Likely) Benign	#117733
9	153	(Likely) Benign	#117733
9	334	(Likely) Benign	#117733
16	77	(Likely) Benign	#117733
19	127	(Likely) Benign	#117733
3	125	(Likely) Benign	#117733
4	9	(Likely) Benign	#117733
7	81	(Likely) Benign	#117733
9	33	(Likely) Benign	#117733
9	50	(Likely) Benign	#117733
9	226	(Likely) Benign	#117733
17	61	(Likely) Benign	#117733
3	65	(Likely) Benign	#117733
4	29	(Likely) Benign	#117733
4	272	(Likely) Benign	#117733
5	59	(Likely) Benign	#117733
5	83	(Likely) Benign	#117733
8	49	(Likely) Benign	#117733
8	88	(Likely) Benign	#117733
9	70	(Likely) Benign	#117733
9	97	(Likely) Benign	#117733
9	217	(Likely) Benign	#117733
10	110	(Likely) Benign	#117733
11	25	(Likely) Benign	#117733
12	93	(Likely) Benign	#117733
13	15	(Likely) Benign	#117733
14	25	(Likely) Benign	#117733
15	39	(Likely) Benign	#117733
16	98	(Likely) Benign	#117733
17	34	(Likely) Benign	#117733
17	67	(Likely) Benign	#117733
18	5	(Likely) Benign	#117733
18	6	(Likely) Benign	#117733
18	83	(Likely) Benign	#117733
18	176	(Likely) Benign	#117733
3	453	(Likely) Pathogenic	#882255
8	89	(Likely) Pathogenic	#882255
13	90	(Likely) Pathogenic	#882255
16	40	(Likely) Pathogenic	#882255
18	146	(Likely) Pathogenic	#882255
19	36	(Likely) Pathogenic	#882255
5	82	(Likely) Pathogenic	#882255
10	139	(Likely) Pathogenic	#882255
10	162	(Likely) Pathogenic	#882255
11	86	(Likely) Pathogenic	#882255
14	66	(Likely) Pathogenic	#882255
15	29	(Likely) Pathogenic	#882255
15	46	(Likely) Pathogenic	#882255
16	21	(Likely) Pathogenic	#882255
16	49	(Likely) Pathogenic	#882255
16	57	(Likely) Pathogenic	#882255
17	39	(Likely) Pathogenic	#882255
17	55	(Likely) Pathogenic	#882255
18	45	(Likely) Pathogenic	#882255
18	99	(Likely) Pathogenic	#882255
4	56	(Likely) Pathogenic	#882255
5	23	(Likely) Pathogenic	#882255
5	103	(Likely) Pathogenic	#882255
7	45	(Likely) Pathogenic	#882255
7	64	(Likely) Pathogenic	#882255
8	90	(Likely) Pathogenic	#882255
9	188	(Likely) Pathogenic	#882255
9	224	(Likely) Pathogenic	#882255
9	253	(Likely) Pathogenic	#882255
10	18	(Likely) Pathogenic	#882255
10	80	(Likely) Pathogenic	#882255
15	63	(Likely) Pathogenic	#882255
15	131	(Likely) Pathogenic	#882255
16	10	(Likely) Pathogenic	#882255
16	30	(Likely) Pathogenic	#882255
19	119	(Likely) Pathogenic	#882255
3	23	Other	black
3	54	Other	black
3	69	Other	black
3	124	Other	black
3	156	Other	black
3	157	Other	black
3	169	Other	black
3	175	Other	black
3	207	Other	black
3	240	Other	black
3	273	Other	black
3	284	Other	black
3	420	Other	black
3	438	Other	black
3	466	Other	black
4	38	Other	black
4	84	Other	black
4	103	Other	black
4	106	Other	black
4	130	Other	black
4	135	Other	black
4	144	Other	black
4	160	Other	black
4	175	Other	black
4	180	Other	black
4	189	Other	black
4	222	Other	black
4	256	Other	black
5	33	Other	black
5	91	Other	black
7	1	Other	black
7	9	Other	black
7	23	Other	black
7	33	Other	black
7	85	Other	black
7	93	Other	black
8	56	Other	black
9	2	Other	black
9	3	Other	black
9	12	Other	black
9	27	Other	black
9	51	Other	black
9	110	Other	black
9	132	Other	black
9	137	Other	black
9	150	Other	black
9	155	Other	black
9	192	Other	black
9	218	Other	black
9	263	Other	black
9	294	Other	black
10	165	Other	black
11	78	Other	black
11	93	Other	black
12	26	Other	black
12	106	Other	black
13	35	Other	black
13	89	Other	black
13	91	Other	black
15	36	Other	black
15	63	Other	black
16	100	Other	black
17	39	Other	black
17	51	Other	black
17	83	Other	black
17	111	Other	black
17	114	Other	black
18	46	Other	black
18	108	Other	black
18	119	Other	black
18	174	Other	black
18	176	Other	black
18	180	Other	black
19	157	Other	black
19	167	Other	black
3	343	Other	black
7	65	Other	black
3	58	Other	black
9	364	Other	black
17	66	Other	black