Details
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Type:
Epic
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Epic Name:Improve VCF in IGB
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Story Points:0.25
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Sprint:Fall 1, Spring 1, Spring 2, Spring 3, Spring 4, Spring 5, Spring 6, Spring 7, Spring 8, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Fall 2, Fall 3, Fall 4, Fall 5, Fall 6, Fall 7, Fall 8, Fall 9, Spring 1, Spring 2, Spring 3
Description
Link to working VCF folder: https://drive.google.com/drive/folders/1Besca3nbUVhv74l4cW7VSZrgugylngPq?usp=drive_link
Situation: IGB currently has the ability to parse a type of file called VCF (Variant Call Format) which contains information about DNA sequence variants. However, we've encountered user-reported issues in the past of IGB being unable to view VCF files due to their version number and it's been a number of years since we've looked at this parser. We would eventually like to work on a new type of visualization in IGB that involves VCF files, so digging into the codebase and ensuring that IGB can handle VCF files is our first step towards doing so.
Task: Check if there's an updated VCF parser that we can use and, if so, upgrade the VCF parser currently implemented in IGB. See the File Formats page in IGB's smoke-testing documentation for a test VCF file as well as instructions for visualizing that file in IGB: https://wiki.bioviz.org/confluence/display/ITD/File+Formats
To learn more about VCF files, here are some links to documentation and explanatory videos:
Attachments
Activity
VCF Documentation: https://github.com/samtools/hts-specs/blob/master/VCFv4.5.pdf
Allele definition: https://www.genome.gov/genetics-glossary/Allele
IGV Desktop Application website download: https://igv.org/
IGV codebase: https://github.com/igvteam/igv
Description of VCF from UCSC: https://genome.ucsc.edu/goldenPath/help/vcf.html
GA4GH website for VCF: https://www.ga4gh.org/product/genetic-variation-formats-vcf/
Actionable items?
- Who is developing VCF?
- What is most recent version of VCF?
- Can we find an example version of a VCF file that is up to date?
- How are we parsing VCF files in IGB (are we using a library, or do we have custom code?)
- How is IGV parsing VCF files?
We've created a Google Drive folder for this project called VCF: https://drive.google.com/drive/folders/1Besca3nbUVhv74l4cW7VSZrgugylngPq?usp=drive_link
This folder currently contains a PowerPoint document (VCF-issues.pptx) which outlines numerous issues with the way IGB is currently displaying VCF files, as well a zipped folder from a previous IGV workshop (igvData.zip) which contains a VCF file that can be used for testing. Here's a link to where I originally accessed those IGV workshop materials: https://www.igv.org/workshops/NCIApril2017/
To view this VCF file in IGB, follow these instructions:
1. Navigate to https://www.igv.org/workshops/NCIApril2017/
2. Download igvData.zip to your computer
3. Extract the contents of igvData.zip
4. Open IGB
5. Open H_sapiens_Feb_2009
6. Open igvData > vcf > ALL.apol1.sample.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf
7. Navigate to APOL1 using the search bar
8. Click Load Data
To view this VCF file in IGV, follow these instructions:
1. Navigate to https://www.igv.org/workshops/NCIApril2017/
2. Download igvData.zip to your computer
3. Extract the contents of igvData.zip
4. Open IGV on your desktop
5. Click File > Open Session
6. Open igvData > vcf > vcf_session.xml
7. Drag and drop the .vcf and .bed files into IGV