<p>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. </p>

CC BY-SA 4.0
2020-05-21T09:25:45.887Z
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!
PedroD
CC BY-SA 4.0
2020-05-21T09:34:15.837Z
I think this one does what I want (http://www.ensembl.org/Homo_sapiens/Tools/VEP), but is giving me "bad gateway".

Any chance this is an open source project?
PedroD
CC BY-SA 4.0
2020-05-21T09:36:59.117Z
Found it: https://github.com/Ensembl/ensembl-vep
PedroD
CC BY-SA 4.0
2020-06-20T00:07:43.137Z
Yes vcf, a discussion on vcf algorithms would be cool
M__
CC BY-SA 4.0
2020-05-20T23:48:37.423Z
2020-05-20T23:48:37.423Z
user8893
<p>I am using a Genome Explorer tool to see all the mutations on my own DNA.</p>

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

<p>Here are a few screenshots:</p>

<p><a href="https://i.sstatic.net/XuJI6.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/XuJI6.png" alt="enter image description here"></a></p>

<p><a href="https://i.sstatic.net/OL31u.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/OL31u.png" alt="enter image description here"></a></p>

<p>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...</p>

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

<p>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.</p>

<p>The closest thing I've found was Geneious: </p>

<p><a href="https://i.sstatic.net/ZECl7.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ZECl7.jpg" alt="enter image description here"></a></p>

<p>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.</p>

<p>Are there any alternatives? Even paying?</p>

<snp><ngs><variant-calling><phylogenetics><indel>
How can I extract all known mutations of my BAM (or SNP/INDL files)?
# How can I extract all known mutations of my BAM (or SNP/INDL files)?

(Asked by: username_0 on 2020-05-20)

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](https://i.sstatic.net/XuJI6.png)](https://i.sstatic.net/XuJI6.png)

[![enter image description here](https://i.sstatic.net/OL31u.png)](https://i.sstatic.net/OL31u.png)

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:

[![enter image description here](https://i.sstatic.net/ZECl7.jpg)](https://i.sstatic.net/ZECl7.jpg)

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?

**Tags:** snp, ngs, variant-calling, phylogenetics, indel

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## 1 answers

### Answer by username_1 on 2020-05-20. Score: 1

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.

> **Comments:**
> **username_0**: 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!  
> **username_0**: I think this one does what I want (http://www.ensembl.org/Homo_sapiens/Tools/VEP), but is giving me "bad gateway".  Any chance this is an open source project?  
> **username_0**: Found it: https://github.com/Ensembl/ensembl-vep  
> **username_2**: Yes vcf, a discussion on vcf algorithms would be cool  

---

