Body: <p><em>This question has also been asked on <a href="https://www.biostars.org/p/9546317/" rel="nofollow noreferrer">Biostars</a></em></p>
  <p>Hi, I am very new to this area, and I am taking a class about bioinformatics. For an independent project assignment, I need to do a GWAS. I am using the bash terminal. I downloaded all the fastq I need,</p>
  <ul>
  <li>trimmed the files,</li>
  <li>converted them into bam/sam</li>
  <li>then performed vcf</li>
  <li>and then bed/bim/fam etc.</li>
  </ul>
  <p>However, when I tried to perform GWAS in plink, I realized I dont have phenotype data. It supposed to have two phenotypes.</p>
  <p>There are two groups/phenotypes of fastq files, each containing 29 samples. Let's say they are group 1 and 2.</p>
  <p>For each group, I converted every fastq to <code>sam</code> then <code>bam</code>, then I combined 29 bam to one bam. Then I combined two bams (for the two groups) together to a vcf.gz.</p>
  <p><strong>Problem.</strong> There is no phenotype data in the following plink files.</p>
  <p><strong>Questions</strong>
  What step has been wrong?
  Or what I should do to incorporate the phenotype data?</p>
  <p>I dont have to be perfect (like the QC steps), and I cannot understand too complicated codes. I am seeking a simple output such as a Manhattan plot or alternative pipeline.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-24T20:34:39.430Z
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: 2022-11-25T23:23:47.463Z
Comments.Text: Please show the command lines you have run. You've asked a question about what step was wrong, but that's difficult to work out without knowing precise details about what you did.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-26T04:19:36.253Z
Comments.Text: Do you _have_ phenotypic data associated with the samples? As noted on the biostars answer, you might need to not combine BAMs such that the relation of each sample with phenotype is maintained.
Comments.UserDisplayName: Maximilian Press
Tags: <sam><vcf><gwas><homework>
Title: Help sought with GWAS and vcf files, lack phenotype labels
ThreadText: # Help sought with GWAS and vcf files, lack phenotype labels
  
  (Asked by: username_0 on 2022-11-24)
  
  *This question has also been asked on [Biostars](https://www.biostars.org/p/9546317/)*
  
  Hi, I am very new to this area, and I am taking a class about bioinformatics. For an independent project assignment, I need to do a GWAS. I am using the bash terminal. I downloaded all the fastq I need,
  
  * trimmed the files,
  * converted them into bam/sam
  * then performed vcf
  * and then bed/bim/fam etc.
  
  However, when I tried to perform GWAS in plink, I realized I dont have phenotype data. It supposed to have two phenotypes.
  
  There are two groups/phenotypes of fastq files, each containing 29 samples. Let's say they are group 1 and 2.
  
  For each group, I converted every fastq to `sam` then `bam`, then I combined 29 bam to one bam. Then I combined two bams (for the two groups) together to a vcf.gz.
  
  **Problem.** There is no phenotype data in the following plink files.
  
  **Questions**
  What step has been wrong?
  Or what I should do to incorporate the phenotype data?
  
  I dont have to be perfect (like the QC steps), and I cannot understand too complicated codes. I am seeking a simple output such as a Manhattan plot or alternative pipeline.
  
  **Tags:** sam, vcf, gwas, homework
  
  > **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**: Please show the command lines you have run. You've asked a question about what step was wrong, but that's difficult to work out without knowing precise details about what you did.  
  > **username_3**: Do you _have_ phenotypic data associated with the samples? As noted on the biostars answer, you might need to not combine BAMs such that the relation of each sample with phenotype is maintained.  
  
  ---
  
  ## 0 answers
  
  