Answers.Body: <p>I can answer the question fairly quickly. You can't as the question is written at the moment.</p>
  <p>The genetic indices you are describing are restricted to comparisons of homologous sites, i.e. strict homologues and that is every index. Direct comparisons between chromosomes, which is how the question is written, violate the assumptions.</p>
  <p>Basically you can use genetic distance TajimaDv, Fst  (fixation index) and other F stats plus linkage disequilibrium, between e.g. &quot;locus x, y, z&quot; chromosome 1 of one individual to &quot;locus x, y,z&quot; of chromosome 1 in another individual (you need a sample size &gt;10 for a valid analysis). Really it should be allele x, y, z (true homologues) which is the output of GATK. However, an intragenomic analysis using these approaches is not viable.</p>
  <hr />
  <p>If the above was your original project, i.e. you'd 10 or more samples, and simply wasn't described accurately, please edit your question with the missing details.</p>
  
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Answers.Text: @M_ Thank you so much for your detailed explanation. I only have reads from chromosomes that belong to the same species. My goal is to find out which chromosome is more similar. I will not be able to achieve my goal with these reads. Is that correct? Any other options?
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Answers.Text: Yes, however if you ask a new question I will explain how you indirectly achieve this aim via a cohort of multiple samples. Please give a bit of background about the aims of the comparison, i.e. the sample and what information you want because you need to establish a representative cohort.
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Body: <p><em>This question was also asked on <a href="https://www.biostars.org/p/9597986/" rel="nofollow noreferrer">Biostars</a></em></p>
  <p>I have the illumina paired end reads of four chromosomes in fastq format. Using the cat command, I merged all of the fastq files into one. I used the GATK hard filtering method to extract SNPs in vcf format after mapping with bwa mem. Next, I would like to find the nucleotide diversity, TajimaD, Fixation index etc from the SNPs. For example, find the diversity between chromosomes 1 and 2, chromosomes 1 and 3, and chromosomes 1 and 4. I would like to know whether this approach is correct. How do I find the above parameters from vcf files or any other methods possible?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-01T13:39:13.103Z
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
Tags: <r><vcf><snp><genomics>
Title: Nucleotide diversity and TajimaD from SNPs
ThreadText: # Nucleotide diversity and TajimaD from SNPs
  
  (Asked by: username_0 on 2024-07-01)
  
  *This question was also asked on [Biostars](https://www.biostars.org/p/9597986/)*
  
  I have the illumina paired end reads of four chromosomes in fastq format. Using the cat command, I merged all of the fastq files into one. I used the GATK hard filtering method to extract SNPs in vcf format after mapping with bwa mem. Next, I would like to find the nucleotide diversity, TajimaD, Fixation index etc from the SNPs. For example, find the diversity between chromosomes 1 and 2, chromosomes 1 and 3, and chromosomes 1 and 4. I would like to know whether this approach is correct. How do I find the above parameters from vcf files or any other methods possible?
  
  **Tags:** r, vcf, snp, genomics
  
  > **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.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-07-01. Score: 0 | Accepted answer
  
  I can answer the question fairly quickly. You can't as the question is written at the moment.
  
  The genetic indices you are describing are restricted to comparisons of homologous sites, i.e. strict homologues and that is every index. Direct comparisons between chromosomes, which is how the question is written, violate the assumptions.
  
  Basically you can use genetic distance TajimaDv, Fst (fixation index) and other F stats plus linkage disequilibrium, between e.g. "locus x, y, z" chromosome 1 of one individual to "locus x, y,z" of chromosome 1 in another individual (you need a sample size >10 for a valid analysis). Really it should be allele x, y, z (true homologues) which is the output of GATK. However, an intragenomic analysis using these approaches is not viable.
  
  ---
  
  If the above was your original project, i.e. you'd 10 or more samples, and simply wasn't described accurately, please edit your question with the missing details.
  
  > **Comments:**
  > **username_0**: @M_ Thank you so much for your detailed explanation. I only have reads from chromosomes that belong to the same species. My goal is to find out which chromosome is more similar. I will not be able to achieve my goal with these reads. Is that correct? Any other options?  
  > **username_2**: Yes, however if you ask a new question I will explain how you indirectly achieve this aim via a cohort of multiple samples. Please give a bit of background about the aims of the comparison, i.e. the sample and what information you want because you need to establish a representative cohort.  
  
  ---
  
  