How to combine multiple vcfs as single using dnanexus

Akhil Pampana

Hello,

I am trying to combine structural variants information for multiple individuals into a single file to perform a gwas analysis. Is there a tutorial on how to combine the files needed?

Regards

Akhil 

Comments

3 comments

Date Votes
  • Comment author
    Akhil Pampana

    Any response would be greatly appreciated?

    0
  • Comment author
    George F The helpers that keep the community running smoothly. UKB Community team Data Analyst

    We do not currently have a tutorial on how to do this but bcftools merge or plink are commonly used programs. The resulting file may to be very large so it filtering for relevant samples or regions may help. 

    0
  • Comment author
    Akhil Pampana

    Hello George F Thank you so much for the response. I am trying to merge the files for only 45k individuals and Structural variants call set. When I am trying to merge I am getting a format exec error. Sample code: bcftools merge -m none --file-list files_to_be_merged_sv_08052024_v2.in --force-samples -Oz -o chr22.vcf.gz

    root@job-GpjVPY0J457kxJJGx9bQfbPB:~# bcftools merge -m none --file-list filelist --force-samples -Oz -o ~/chr22.vcf.gz
    [E::hts_hopen] Failed to open file vcf.gz.tbi
    [E::hts_open_format] Failed to open file vcf.gz.tbi" : Exec format error
    Failed to open dragen.sv.vcf.gz.tbi: Exec format error
     

    Have seen this error before if so could you able to help me out regarding this? 

    0

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