Answers.Body: <p>This looks like genotyping failed for some samples. It's unclear from the op whether the genotyping data was controlled for quality, but I would recommend performing sample QC.</p>
  <p>On a side note: in human gwas with imputed snps, I would expect to see clusters of significant snps as a sign that the significant snps are not an artifact. In the op there are some single significant snps. This might be a sign that those significant snps are artifacts. There are also some snps that form clusters and therefore look more promising.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-21T07:28:43.197Z
Answers.Text: Ok, I see. Thank you very much for your answer. QC was not performed, going to do this now.
Answers.UserDisplayName: snowflake
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-19T15:05:30.100Z
Answers.Text: Follow up question:https://bioinformatics.stackexchange.com/questions/14398/interpreting-gwas-results-with-different-settings
Answers.UserDisplayName: snowflake
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-21T07:21:06.680Z
Answers.LastActivityDate: 2020-08-21T07:21:06.680Z
Answers.UserDisplayName: winni2k
Body: <p>I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~ 3.8 which shows a strange pattern (many dots in one line with same value).</p>
  <p><a href="https://i.sstatic.net/w9x4I.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/w9x4I.png" alt="enter image description here" /></a></p>
  <p>If I increase the filter to 6 % the dots in a line disappear but I loose also some significant SNPs:</p>
  <p><a href="https://i.sstatic.net/4tMdD.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/4tMdD.png" alt="enter image description here" /></a></p>
  <p>Sample are about 77000 SNP positions (barley), unimputed from GWAS (all NaNs removed). GWAS was performed with 200 phenotype samples.</p>
  <p>How to interpret the dots in  a line?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-21T06:33:39.750Z
Comments.Text: I updated my question.
Comments.UserDisplayName: snowflake
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-21T06:44:11.467Z
Comments.Text: Thanks. How many samples and what organism? I assume this is a snp chip?
Comments.UserDisplayName: winni2k
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-21T07:04:26.257Z
Comments.Text: Barley with 200 phenotypes.
Comments.UserDisplayName: snowflake
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-21T07:23:42.603Z
Comments.Text: There seems to be something wrong with the Manhattan plots: snps from different chromosomes are overlapping? For example, green does can be found inside the region for red dots.
Comments.UserDisplayName: winni2k
Tags: <python><gwas>
Title: GWAS MAC filter Interpretation
ThreadText: # GWAS MAC filter Interpretation
  
  (Asked by: username_0 on 2020-08-19)
  
  I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~ 3.8 which shows a strange pattern (many dots in one line with same value).
  
  [![enter image description here](https://i.sstatic.net/w9x4I.png)](https://i.sstatic.net/w9x4I.png)
  
  If I increase the filter to 6 % the dots in a line disappear but I loose also some significant SNPs:
  
  [![enter image description here](https://i.sstatic.net/4tMdD.png)](https://i.sstatic.net/4tMdD.png)
  
  Sample are about 77000 SNP positions (barley), unimputed from GWAS (all NaNs removed). GWAS was performed with 200 phenotype samples.
  
  How to interpret the dots in a line?
  
  **Tags:** python, gwas
  
  > **Comments:**
  > **username_0**: I updated my question.  
  > **username_1**: Thanks. How many samples and what organism? I assume this is a snp chip?  
  > **username_0**: Barley with 200 phenotypes.  
  > **username_1**: There seems to be something wrong with the Manhattan plots: snps from different chromosomes are overlapping? For example, green does can be found inside the region for red dots.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-08-21. Score: 1 | Accepted answer
  
  This looks like genotyping failed for some samples. It's unclear from the op whether the genotyping data was controlled for quality, but I would recommend performing sample QC.
  
  On a side note: in human gwas with imputed snps, I would expect to see clusters of significant snps as a sign that the significant snps are not an artifact. In the op there are some single significant snps. This might be a sign that those significant snps are artifacts. There are also some snps that form clusters and therefore look more promising.
  
  > **Comments:**
  > **username_0**: Ok, I see. Thank you very much for your answer. QC was not performed, going to do this now.  
  > **username_0**: Follow up question:https://bioinformatics.stackexchange.com/questions/14398/interpreting-gwas-results-with-different-settings  
  
  ---
  
  