Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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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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Story Points:4
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Epic Link:
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Sprint:Spring 3, Spring 5, Spring 6, Spring 8, Summer 1
Description
Situation: Collect vcf files for testing changes
Task: Gather and test vcf files
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3836 [ 23135 ] |
| Description |
Situation: loaders depends on LineProcessor for parsing and loading genomic regions
Task: Investigate how we could eliminate the LineProcessor dependency completely, streamlining the parsing process and displaying region. |
Situation: Collect vcf files for testing changes
Task: Gather vcf files |
| Attachment | vcf_sample_files.zip [ 18661 ] |
| Sprint | Spring 3, Spring 5 [ 212, 214 ] | Spring 3, Spring 5, Spring 6 [ 212, 214, 215 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Note: It seems like there are an array of different indexes being used with vcf/bcf files. For example, Genome in a Bottle has a gzipped vcf with a .tbi index. If using bcftools you can specify --write-index which will output either a "tbi" or "csi" depending on output file format.
| Summary | Collect VCF files for testing changes | Collect VCF files and test new vcf parsing |
| Description |
Situation: Collect vcf files for testing changes
Task: Gather vcf files |
Situation: Collect vcf files for testing changes
Task: Gather and test vcf files |
Testing all other file formats: https://wiki.bioviz.org/confluence/display/ITD/File+Formats
| Sprint | Spring 3, Spring 5, Spring 6 [ 212, 214, 215 ] | Spring 3, Spring 5, Spring 6, Spring 7 [ 212, 214, 215, 216 ] |
| Rank | Ranked higher |
Current implementation is failing when trying to load VCF from Quickload
Issue eloboration:
New implementation has VCFFileReader, which can process only local files not any kind of URL (http)
| Sprint | Spring 3, Spring 5, Spring 6, Spring 7 [ 212, 214, 215, 216 ] | Spring 3, Spring 5, Spring 6, Spring 8 [ 212, 214, 215, 217 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Spring 3, Spring 5, Spring 6, Spring 8 [ 212, 214, 215, 217 ] | Spring 3, Spring 5, Spring 6, Spring 8, Summer 1 [ 212, 214, 215, 217, 218 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
This ticket can be considered complete as we have collected VCF files and tested them. The primary issue that was identified is that the current implementation is not working to load files from the web (http/https for example). IGBF-4219 was created to fix this issue.
Closing ticket.
| Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
I took the two files that we had found earlier and subset the larger file to just APOL1. Note that one sample vcf is for the 2013 human genome and the other is for the 2009 human genome (see the respective readme.txt files). I also created multiple indexes for the files using tabix, bcftools, or igvtools. The files themselves are either raw or bgzipped.
There are also two bcf files, but I could not get them to load in either IGB or IGV,
so something seems wrong with them(based on this comment it does not appear that IGV supports BCF files, so the attached BCF files are probably valid).