plink --merge-list gives wrong chromosome annotations. GWAS tutorial.

When I run plink merge “plink --merge-list files_to_merge.txt --make-bed --autosome-xy --out ukb22418_c1_22_v2_merged” I get chromosomes 23, 24, 26 and 26, which causes an error in downstream regenie. I assume these chromosomes refer to this:

 

X    X chromosome                    -> 23      

Y    Y chromosome                    -> 24      

XY   Pseudo-autosomal region of X    -> 25      

MT   Mitochondrial                   -> 26

 

How do I avoid this when running Plink, and can I just replace the corresponding chromosomes from the bim-file?

I followed the tutorial: https://www.youtube.com/watch?v=762PVlyZJ-U&t=2604s

Comments

2 comments

  • Comment author
    George F The helpers that keep the community running smoothly. UKB Community team Data Analyst

    If you want to merge just the autosomes, don't include the relevant chromosomes in the files_to_merge.txt.

    I assume the command you're following is from 34:00 in the video.

    You can just edit the first line of command ie 

    run_merge="cp /mnt/project/Bulk/Genotype\ Results/Genotype\ calls/ukb22418_c{1..22}_b0_v2* .; ls  *.bed | sed -e 's/.bed//g' > files_to_merge.txt;

     

     

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  • Comment author
    Tamrat Befekadu Abebe

    Hi, 

    I am also facing some issues while executing the command line interface to merge the binary files. I used the following code 

    #!/bin/sh

    run_merge="cp /mnt/project/Bulk/Genotype\ Results/Genotype\ calls/ukb22418_c{1..22}_b0_v2* .; ls *.bed | sed -e 's/.bed//g' > files_tp_merge.txt; \
    > plink --merge-list files_to_merge.txt --make-bed --autosome-xy --out ukb22418_c1_c22_v2_merged; rm files_to_merge.txt;"
     

    dx run swiss-army-knife -iin="/Data/main_wes_450k.phe" -icmd="${run_merge}" --tag="Step1" --instance-type "mem1_ssd1_v2_x16" --destination="/Data/" --brief --yes

     

    When I execute the above line of code in Git Bash, I always get the following ResolutionError.

    dxpy.utils.resolver.ResolutionError: Could not find a project named “C”

     

    I directly typed the code in Git Bash also tried saving the shell script in the PATH directory and call ‘sh partB-merge-files-dxfuse.sh’, but it has the same error message.  

     

    I am not sure where I made an error. 

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