Answers.Body: <p>The ancestral allele is not always the reference allele. Ref and alt aren't switched, ref is just rare in at least the population you're looking at (it appears to be rare in humans as a whole). So, the C is indeed reference and G is indeed altered, it's just that people homozygous for the G are the overwhelming majority. This is evidenced by the rs477033 variant being named NC_000001.11:g.165890393C&gt;G. So, in short, nothing went wrong, all tools functioned correctly.</p>
  <p>You'll notice a bunch of these over time, either make a database of them (or find one, someone may have made one) and filter them out or see if maybe the 1000 genomes reference genome has some of these modified (or maybe the T2T genome that was recently published).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-06-23T10:23:07.563Z
Answers.Text: I think that I found the solution and I'd like to add it here. It might be helpful for others. I just simply performed additional annotation of my .vcf files using 1KGenomes data. I've found it here: [here](http://ftp.ensembl.org/pub/release-105/variation/vcf/homo_sapiens/) Then each variant is described in `INFO` by `AA` which means ancestral allele. If this allele is different comparing to my `REF` I filter it out.
Answers.UserDisplayName: Adamm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-04-22T14:20:08.253Z
Answers.LastActivityDate: 2022-04-22T14:20:08.253Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag 'COMMON=0' and very low MAF. I also checked the .bam file (in IGV) and this rs itself in <a href="https://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=1:165889893-165890893;v=rs477033;vdb=variation;vf=248830" rel="nofollow noreferrer">ensembl</a> database. It looks like this:</p>
  <p><a href="https://i.sstatic.net/Iy364.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Iy364.png" alt="igv" /></a></p>
  <p>The problem is: in this case ref and alt are switched. The G is reference (ancestral) allele and C is altered. Nevertheless in the .bam file it's interpreted in opposite way. Of course it's false positive variant - there's no mutation there at all. All variant callers returned it as high quality variant. My. bam files are full of them.</p>
  <p><strong>What went wrong in this case? Problem with mapping?</strong></p>
  <p><strong>How can I fix this thing, to get only novel and rare true positive variants?</strong></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-26T01:34:01.497Z
Comments.Text: [link] https://drive.google.com/file/d/1eheG5MqS_a1xK5HSqsNJ0Tito_WdL_YV/view?usp=sharing
Comments.UserDisplayName: envs_h_gang_5
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-26T01:36:29.463Z
Comments.Text: A reference sequence can obviously not represent all populations,  as shown above in the linked chapter (• page 30 •),  a reference allele may be the minor allele in the population you are studying ( in some cases )
Comments.UserDisplayName: envs_h_gang_5
Tags: <sam><snp><ngs><variant-calling>
Title: Reference variant detected as altered one in bam file
ThreadText: # Reference variant detected as altered one in bam file
  
  (Asked by: username_0 on 2022-04-22)
  
  I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag 'COMMON=0' and very low MAF. I also checked the .bam file (in IGV) and this rs itself in [ensembl](https://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=1:165889893-165890893;v=rs477033;vdb=variation;vf=248830) database. It looks like this:
  
  [![igv](https://i.sstatic.net/Iy364.png)](https://i.sstatic.net/Iy364.png)
  
  The problem is: in this case ref and alt are switched. The G is reference (ancestral) allele and C is altered. Nevertheless in the .bam file it's interpreted in opposite way. Of course it's false positive variant - there's no mutation there at all. All variant callers returned it as high quality variant. My. bam files are full of them.
  
  **What went wrong in this case? Problem with mapping?**
  
  **How can I fix this thing, to get only novel and rare true positive variants?**
  
  **Tags:** sam, snp, ngs, variant-calling
  
  > **Comments:**
  > **username_1**: [link] https://drive.google.com/file/d/1eheG5MqS_a1xK5HSqsNJ0Tito_WdL_YV/view?usp=sharing  
  > **username_1**: A reference sequence can obviously not represent all populations,  as shown above in the linked chapter (• page 30 •),  a reference allele may be the minor allele in the population you are studying ( in some cases )  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-04-22. Score: 3 | Accepted answer
  
  The ancestral allele is not always the reference allele. Ref and alt aren't switched, ref is just rare in at least the population you're looking at (it appears to be rare in humans as a whole). So, the C is indeed reference and G is indeed altered, it's just that people homozygous for the G are the overwhelming majority. This is evidenced by the rs477033 variant being named NC\_000001.11:g.165890393C>G. So, in short, nothing went wrong, all tools functioned correctly.
  
  You'll notice a bunch of these over time, either make a database of them (or find one, someone may have made one) and filter them out or see if maybe the 1000 genomes reference genome has some of these modified (or maybe the T2T genome that was recently published).
  
  > **Comments:**
  > **username_0**: I think that I found the solution and I'd like to add it here. It might be helpful for others. I just simply performed additional annotation of my .vcf files using 1KGenomes data. I've found it here: [here](http://ftp.ensembl.org/pub/release-105/variation/vcf/homo_sapiens/) Then each variant is described in `INFO` by `AA` which means ancestral allele. If this allele is different comparing to my `REF` I filter it out.  
  
  ---
  
  