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.

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)

Testing all other file formats: https://wiki.bioviz.org/confluence/display/ITD/File+Formats

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.

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).