Body: <p>I have performed NGS on 34 patient samples and 11 controls. Now I have variants from both groups but there is obvious difference in number of variants.
  How can I compare variants of both groups statistically?
  Can I do association analysis?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-14T09:29:10.847Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-14T16:00:58.227Z
Comments.Text: This is simply a GWAS calculation. You can do this via phylogenetics, it's very complicated, but it will work. HOWEVER, I am assuming this is a whole genome NGS (*variants* so it must be), rather than RNAseq. RNAseq is a very different calculation. It would be useful to specify the disease because there will be prior variant association studies.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-14T20:58:27.207Z
Comments.Text: Please explain more about your experiment and desired analysis. What platform was sequencing done on? What coverage? How do you know you have variants in both groups? What additional processing has been done on the FASTQ files to demonstrate that there are variants?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-17T07:23:32.133Z
Comments.Text: Mitochondrial DNA sequencing on Illumina platform and analysis was performed using bwa-mem, bcftools and Mitomap for variant annotation. I want to compare DNA variants in both groups (34 patients, 11 controls) and any association of these variants with disease. Can population specific Allele frequency from gnomAD help in analysis of rare variants?
Comments.UserDisplayName: S_Malik
Tags: <ngs><r><sequence-analysis><variants>
Title: What statistical analysis should I perform on DNA variants from unequal number of case (34) and control (11) samples?
ThreadText: # What statistical analysis should I perform on DNA variants from unequal number of case (34) and control (11) samples?
  
  (Asked by: username_0 on 2023-06-14)
  
  I have performed NGS on 34 patient samples and 11 controls. Now I have variants from both groups but there is obvious difference in number of variants.
  How can I compare variants of both groups statistically?
  Can I do association analysis?
  
  **Tags:** ngs, r, sequence-analysis, variants
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: This is simply a GWAS calculation. You can do this via phylogenetics, it's very complicated, but it will work. HOWEVER, I am assuming this is a whole genome NGS (*variants* so it must be), rather than RNAseq. RNAseq is a very different calculation. It would be useful to specify the disease because there will be prior variant association studies.  
  > **username_3**: Please explain more about your experiment and desired analysis. What platform was sequencing done on? What coverage? How do you know you have variants in both groups? What additional processing has been done on the FASTQ files to demonstrate that there are variants?  
  > **username_0**: Mitochondrial DNA sequencing on Illumina platform and analysis was performed using bwa-mem, bcftools and Mitomap for variant annotation. I want to compare DNA variants in both groups (34 patients, 11 controls) and any association of these variants with disease. Can population specific Allele frequency from gnomAD help in analysis of rare variants?  
  
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  ## 0 answers
  
  