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I am using a Genome Explorer tool to see all the mutations on my own DNA.

My particular interest is on listing the variants and get their names/ids.

Here are a few screenshots:

enter image description here

enter image description here

You can see that they tell you the genomic position, the allele frequency of the mutation, the name of the disease, the Category, etc etc...

However, the filters on this tool work very badly so I cannot filter all my mutations only...

So I was trying to find out an alternative tool to get this data in such a nice way this tool provides. I tried IGV but they just provide raw readings, I didnt find a way to get a list of variants the same way this Genome Explorer does.

The closest thing I've found was Geneious:

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but it crashes on my computer and is too complex to use (I wasn't able to reach that screen above, from my BAM file). And it also eats a lot of RAM that I don't have.

Are there any alternatives? Even paying?

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If you have a BAM file, you could easily run a variant caller analysis software such as freebayes, though you would need a good amount of computing power like a cluster or a dedicated node with good memory. Freebayes outputs a vcf file that has all the variants listed. Then you can load it into the UCSC or Ensembl human genome browsers and look at what genes they are.

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  • $\begingroup$ Hi! Thank you for sharing! I already have these files as well actually (.snp.vcf.gz, .indel.vcf.gz, .cnv.vcf.gz and their .tbi's). Can you detail me a bit more on the part where I can load these into some tools to list all mutations known to mankind at current 2020 (and their related disease/classification)? I am exploring both websites you just mentioned but feeling a bit lost. Thanks! $\endgroup$
    – PedroD
    Commented May 21, 2020 at 9:25
  • $\begingroup$ I think this one does what I want (ensembl.org/Homo_sapiens/Tools/VEP), but is giving me "bad gateway". Any chance this is an open source project? $\endgroup$
    – PedroD
    Commented May 21, 2020 at 9:34
  • $\begingroup$ Found it: github.com/Ensembl/ensembl-vep $\endgroup$
    – PedroD
    Commented May 21, 2020 at 9:36
  • $\begingroup$ Yes vcf, a discussion on vcf algorithms would be cool $\endgroup$
    – M__ ♦
    Commented Jun 20, 2020 at 0:07

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