Answers.Body: <p>If this is your own DNA and you are trying to analyse yourself you should talk to a genetic counselor. I personally think it's cool, but I deeply understand the potential consequences.</p>
  <p>What you want is a variant annotation tool. There are many, but I normally write my own. Which is simply a case of pulling down a database and using pandas to match variants with annotation.</p>
  <p>There are many databases. The biggest popular database is gnomad and the biggest disease database is clinvar. Others include omim, snpdb and 1k genomes. I'm not sure about blood sorry but I'm sure you can find one.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-31T20:34:28.040Z
Answers.LastActivityDate: 2021-01-31T20:34:28.040Z
Answers.UserDisplayName: Liam McIntyre
Body: <p>I bought a &quot;Whole Genome Sequence&quot; kit, which gave me the following VCF files (this service did not include any analysis, just the raw data):</p>
  <p><code>cnv.vcf</code>
  <code>indel.vcf</code>
  <code>snp.vcf</code>
  <code>sv.vcf</code></p>
  <p>My understanding is that these files show the differences of my DNA relative to a reference human genome (hg19 in my case)</p>
  <p>What tools and resources can I use to find out which known alleles/variants of genes I have?</p>
  <h2>An example: Blood type</h2>
  <p>According to <a href="https://en.wikipedia.org/wiki/ABO_(gene)#Common_alleles" rel="nofollow noreferrer">Wikipedia</a>, there are 6 common alleles of the <a href="http://uswest.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000123095;r=12:26120030-26125037" rel="nofollow noreferrer">ABO gene</a>, and which alleles I have determine my blood type.</p>
  <p>Looking at my VCF results, I have these SNPs and INDELs within that gene:</p>
  <pre><code>&lt;removed&gt;
  </code></pre>
  <p>Given this, how would I figure out my blood type?</p>
  <p>I understand that my data may not be 100% accurate, and that many phenotypes are the result of more than one gene, environmental factors, or are not well studied at all, but this should work for some simple things ie blood type, <a href="https://pubmed.ncbi.nlm.nih.gov/17185601/" rel="nofollow noreferrer">COMT</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096202/" rel="nofollow noreferrer">BHLHE41</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/16522833/" rel="nofollow noreferrer">CYP1A2</a>, etc</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-27T10:07:49.063Z
Comments.Text: For the blood locus. Try and find online the genomic position (i.e. the number like 133273540 in the POS field of the .vcf) of the ABO blood locus and look it up on your dataset. Remember to make sure you find it on the gr37/hg19 build.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-27T12:43:32.233Z
Comments.Text: Wait, did you got yourself yourself sequenced?? I thought "my DNA" means "my DNA sample" not "my own DNA"!
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-27T12:53:44.443Z
Comments.Text: And do I get right, you know your variants and you would like to know something about them, right?
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-27T13:26:38.883Z
Comments.Text: Please don't just share your own genetic information online, especially if you are not fully understanding what you are looking at. It is not something to be posted everywhere, although some loci might be relatively harmless you shouldn't take this lightly.
Comments.UserDisplayName: Wouter De Coster
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-27T13:35:01.760Z
Comments.Text: Please ping me if you decide you want this censored. You should be very aware of the long-term consequences for you and your current and future relatives of sharing your genetic information on the internet in a post.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-27T19:06:01.607Z
Comments.Text: @DevonRyan thanks, I've removed it. I didn't think a small snippet would be a problem
Comments.UserDisplayName: Knio
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-27T19:08:05.483Z
Comments.Text: @WouterDeCoster also thanks for the warning
Comments.UserDisplayName: Knio
Tags: <genome><vcf><public-databases><wgs><human-genome>
Title: What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?
ThreadText: # What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?
  
  (Asked by: username_0 on 2021-01-27)
  
  I bought a "Whole Genome Sequence" kit, which gave me the following VCF files (this service did not include any analysis, just the raw data):
  
  `cnv.vcf`
  `indel.vcf`
  `snp.vcf`
  `sv.vcf`
  
  My understanding is that these files show the differences of my DNA relative to a reference human genome (hg19 in my case)
  
  What tools and resources can I use to find out which known alleles/variants of genes I have?
  
  ## An example: Blood type
  
  According to [Wikipedia](https://en.wikipedia.org/wiki/ABO_(gene)#Common_alleles), there are 6 common alleles of the [ABO gene](http://uswest.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000123095;r=12:26120030-26125037), and which alleles I have determine my blood type.
  
  Looking at my VCF results, I have these SNPs and INDELs within that gene:
  
  ```
  <removed>
  
  ```
  
  Given this, how would I figure out my blood type?
  
  I understand that my data may not be 100% accurate, and that many phenotypes are the result of more than one gene, environmental factors, or are not well studied at all, but this should work for some simple things ie blood type, [COMT](https://pubmed.ncbi.nlm.nih.gov/17185601/), [BHLHE41](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096202/), [CYP1A2](https://pubmed.ncbi.nlm.nih.gov/16522833/), etc
  
  **Tags:** genome, vcf, public-databases, wgs, human-genome
  
  > **Comments:**
  > **username_1**: For the blood locus. Try and find online the genomic position (i.e. the number like 133273540 in the POS field of the .vcf) of the ABO blood locus and look it up on your dataset. Remember to make sure you find it on the gr37/hg19 build.  
  > **username_2**: Wait, did you got yourself yourself sequenced?? I thought "my DNA" means "my DNA sample" not "my own DNA"!  
  > **username_2**: And do I get right, you know your variants and you would like to know something about them, right?  
  > **username_3**: Please don't just share your own genetic information online, especially if you are not fully understanding what you are looking at. It is not something to be posted everywhere, although some loci might be relatively harmless you shouldn't take this lightly.  
  > **username_4**: Please ping me if you decide you want this censored. You should be very aware of the long-term consequences for you and your current and future relatives of sharing your genetic information on the internet in a post.  
  > **username_0**: @username_4 thanks, I've removed it. I didn't think a small snippet would be a problem  
  > **username_0**: @username_3 also thanks for the warning  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_5 on 2021-01-31. Score: 1
  
  If this is your own DNA and you are trying to analyse yourself you should talk to a genetic counselor. I personally think it's cool, but I deeply understand the potential consequences.
  
  What you want is a variant annotation tool. There are many, but I normally write my own. Which is simply a case of pulling down a database and using pandas to match variants with annotation.
  
  There are many databases. The biggest popular database is gnomad and the biggest disease database is clinvar. Others include omim, snpdb and 1k genomes. I'm not sure about blood sorry but I'm sure you can find one.
  
  
  ---
  
  