Clinical Annotator of Variants

This app is being upgraded and is not currently available. Instead, please use Data Viewer Plus, which is new functionality at Sequencing.com that provides similar information as this app.

Log in to your Sequencing.com account and click the 'Add to My Apps' button located under the app icon. This app will instantly be added to your account and a 'Start App' button will appear under the app icon.

1. Start the app by clicking the 'Start App' button
   • You can also start the app directly from My Apps
2. Select a VCF file
   • If your file isn't in VCF format you can convert almost any format into VCF using the EvE app.
3. Select the reference genome that was used to generate the VCF file or select 'Auto Detect' and we'll automatically determine the reference genome
4. Most users: Click 'Submit' button.
   • For advanced users: click 'Modify parameters' to view all modifiable parameters. After defining your desired parameters, click 'Submit'.
     • Before clicking Submit you can select to save your modified parameters. If saved, the next time you use this app all parameters will automatically be adjusted to your previously saved parameters.
       • Saves you time because you don't have to define parameters each time you use the app.

 

Once the app finishes you'll receive an email with a link to the results. You can also access results at any time by clicking Apps in the header and then clicking the Results tab.

• The CSV file generated by this app will be securely stored in your account.
  • You can download the file, share it with others and use it with your other apps.

Inputs

• VCF v4.1 file containing human genetic data
• Reference genome used to create the VCF file -OR- select Reference Genome 'Auto Detect' as the reference genome will be automatically determined
• If a specific set of genes is needed, add a genelist.txt file. If this is not added then all genes will be included.
  • File must contain one human gene symbol per row
  • File must be in .txt format
  • Upload your genelist.txt file to your Sequencing.com account and then when you start this app select 'Modify parameters' (appears above the 'Submit' button). Then select the option to define genes and select your genelist.txt file.

Outputs

• CSV file (TAB delimited TXT file)
• Every line of the CSV file represents a single variant call
• CSV file will contain the following columns:

1. ID (Variant call ID taken from the input file)
2. CHROM (chromosome of variant)
3. POS (genomic coordinate of variant)
4. REF (reference allele of variant)
5. ALT (alternative allele of variant)
6. QUAL (QUAL value in the input VCF record)
7. FILTER (FILTER value in the input VCF record)
8. TYPE (value of TYPE annotation flag)
9. ENST (value of ENST annotation flag)
10. GENE (value of GENE annotation flag)
11. TRINFO (value of TRINFO annotation flag)
12. LOC (value of LOC annotation flag)
13. CSN (value of CSN annotation flag)
14. CLASS (value of CLASS annotation flag)
15. SO (value of SO annotation flag)
16. IMPACT (value of IMPACT annotation flag)
17. ALTFLAG (value of ALTFLAG annotation flag)
18. ALTCLASS (value of ALTCLASS annotation flag)
19. ALTSO (value of ALTSO annotation flag)
20. DBSNP (value of DBSNP annotation flag)

Multiallelic calls and/or multiple transcripts

Every line of the output CSV file represents a single variant call. Unlike in the VCF format, annotation information for multiallelic variant calls are split to multiple lines (Example 1). If a variant call overlaps with multiple transcripts, the information is also split into multiple records (Example 2).

Example 1

For the single VCF record describing a 1-base deletion and a 1-base insertion:

#CHROM	POS	ID	REF	ALT	Additional columns...
8	3443799	.	GA	G,GAA	Additional data...

 

two lines will be added to the output CSV file:

ID	CHROM	POS	REF	ALT	QUAL	FILTER	TYPE	ENST	GENE	Additional columns...
.	8	3443799	GA	G	42	PASS	Deletion	ENST00000537824	CSMD1	Additional data...
.	8	3443799	GA	GAA	42	Pass	Insertion	ENST00000537824	CSMD1	Additional data...

 

The TYPE and CSN annotation flags are given as follows:

• TYPE=Deletion,Insertion
• CSN=c.1098-18delT,c.1098-18dupT;

 

Example 2

For the single VCF record describing a triallelic substitution that overlaps with two transcripts (ENST00000325203 and ENST00000344683) in the whole exome set:

#CHROM	POS	ID	REF	ALT	Additional columns...
8	6389889	.	C	G,A	Additional data...

 

four lines will be added to the output CSV file:

ID	CHROM	POS	REF	ALT	QUAL	FILTER	TYPE	ENST	GENE	Additional columns...
.	8	6389889	C	G	200	PASS	SUBSTITUTION	ENST00000325203	ANGPT2	Additional data...
.	8	6389889	C	G	200	PASS	SUBSTITUTION	ENST00000344683	MCPH1	Additional data...
.	8	6389889	C	A	200	PASS	SUBSTITUTION	ENST00000325203	ANGPT2	Additional data...
.	8	6389889	C	A	200	PASS	SUBSTITUTION	ENST00000344683	MCPH1	Additional data...

 

The GENE, LOC and CSN annotation flags are given as follows:

• GENE=ANGPT2:MCPH1,ANGPT2:MCPH1
• LOC=Ex2:In12/13,Ex2:In12/13
• CSN=c.408G>C_p.=:c.2214+32439C>G,c.408G>T_p.=:c.2214+32439C>A
• Note that both alternative alleles in both genes (ANGPT2 and MCPH1) cause synonymous and intronic changes, respectively.

This app utilizes CAVA v1.1.0.

Márton Münz, Elise Ruark, Anthony Renwick, Emma Ramsay, Matthew Clarke, Shazia Mahamdallie, Victoria Cloke, Sheila Seal, Ann Strydom, Gerton Lunter, Nazneen Rahman. (2015) CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting. Genome Medicine 7:76, doi:10.1186/s13073-015-0195-6.