Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Quilt use sample name as input #178

Open
LouisLeNezet opened this issue Feb 2, 2025 · 0 comments · May be fixed by #186
Open

Quilt use sample name as input #178

LouisLeNezet opened this issue Feb 2, 2025 · 0 comments · May be fixed by #186
Labels
bug Something isn't working

Comments

@LouisLeNezet
Copy link
Collaborator

Description of the bug

If the name of the sample in the bam files are equal QUILT will generate a wrongly formatted vcf with multiple times the same sample names, leading in an error in bcftools annotate step.
We need to provide a sampleNames_file in the same order as the bamlist.

Command used and terminal output



Relevant files


No response


System information


No response

      		
    

      
  





        

            


            

              
            

        

      


      
    








      

    



      

  
            

    

      
    

    


      

          @LouisLeNezet
LouisLeNezet




          added
  the 

  bug

  Something isn't working
 label


      Feb 2, 2025

    

  



  

  

    
  


  

      

    @LouisLeNezet
LouisLeNezet



    linked a pull request
    
      Feb 20, 2025
    

    that will
    close
    this issue





  


  

      
   Open

  





  
  

      
        
      
      

  
    
    
  


    11 tasks
  





  




  

  

    
  


  

    


      @LouisLeNezet
LouisLeNezet



        linked a pull request
        Feb 20, 2025
        that will
        close
        this issue





  

    
      Add sampleNames_file option for QUILT and STITCH
      #186
  



  

      
   Open

  





  
  

      
        
      
      

  
    
    
  


    11 tasks
  





  













  
  

    

      

  





  




  
  

              

  
    Sign up for free
    to join this conversation on GitHub.
    Already have an account?
    Sign in to comment


  



  






  
                  




    

  


      
  

    Assignees
  



        

    No one assigned







      


  


  

    Labels
  



    

      

    bug

  Something isn't working








      

  

    

        

    Projects
  


        




    None yet




  



      


  

    
  

    Milestone
  


      No milestone





    
      
          
  

    

      

        
          

            
    

    Development
  




              
  
Successfully merging a pull request may close this issue.





    


  
          
      Add sampleNames_file option for QUILT and STITCH

    
      LouisLeNezet/phaseimpute
    





        
      

    

  


      

    

  
      

  

    

      1 participant
    

    

        
          @LouisLeNezet