Entering edit mode
7.2 years ago
beneficii
▴
60
I'm curious at looking at admixture, but having trouble finding tools that would work with VCF or BAM files. I know there is samtools or bamtools, but it doesn't work, and I can't get vcftools to work in my computer. So are there other tools that would work with these files?
If not, then why did the company put my genome in these file formats in the first place?
Because those are the formats used by nearly everyone, everywhere.
Are there tools other than the samtools, bamtools, and vcftools that will work with them?
I've found IGV works, and can check SNPs with them, which I've found helpful. All I need to do is make sure I get the GRCh37 version of the genetic location.
I heard there are SNPs that are used to check admixture. Is there a list of these SNPs somewhere?
I would estimate that thousands of tools work with vcf and bam files. I'm not sure, but I would expect plink to be a tool which could help you for the admixture question (which is not really specified...).
I ran PLINK on the VCF and it made 3 files with .bed, .bim, and .fam extensions.
However, ADMIXTURE does not have a Windows version.
Oh, that explains why you can't get software working. Make it easier for yourself and get a Linux.
I got an Oracle VM like a year ago, but I can't get it to work anymore. Even though I'm using the same ISO and computer as before, it now says that it can only find a i686 and that it needs a x86-64 CPU. Why I'm getting this error now when I didn't get it before with the same ISO and the exact same computer and OS, I cannot even begin to figure out.
I frequently run into stuff like this that makes no sense, which makes me want to find another way.
You need to sort this out with Oracle VirtualBox, most likely you just need to update it if you want to run a software, you have to fulfill the dependencies. You are not getting very far with the attitude that you are entitled to a version of open source software for any operating system.
Thanks. I got it. But now I have a new issue, but it deserves its own thread.