So, I had my WGS done by Veritas Genetics and it was transferred to the PGP. I will not reveal the account, however, for privacy reasons. Having difficulty finding good software, I came across NCBI Genome Workbench, which seemed complete and accessible.
The PGP account gives a VCF file, as well as several BAM files. As the VCF file is smaller, I tried that first. I tried loading it in Genome Workbench and it went through the process, but after 20 minutes it crashed my computer and I was forced to reboot my system. I tried 3 more times with the same result. I cannot find any sort of troubleshooting documentation for gbench. So it looks like using VCF files was out. For whatever reason, gbench can't work with them.
So I downloaded all the BAM files, and tried working with that. It says I needed samtools to index them, so I browsed to samtools and selected it. And then it asks me some more questions, I just told it to save the graph files. It asks me what indexes I wanted to load, so I just selected all of them. This is where the first issue appears, however, as it seems like all the indexes are repeated for every BAM file I'm adding (1 per chromosome). It seems like perhaps gbench expects everything to be in 1 BAM file. But either way, I thought it was just a fluke or something and continued. And then it ran. After maybe 30 minutes, it was done. I then tried to open the graph files in the Graphical Sequence View file, as the tutorial said to do, but now it says, "Graphical view: failed to retrieve sequence for id lcl|chr1."
It is really difficult to work with these kinds of files, apparently. Apparently, something happened with gbench. Either I did something wrong or it was buggy.
Can anyone help? Neither Help nor Tutorial provides any troubleshooting that I can make sense of.