tidy_vcf function
Entering edit mode
6 months ago
sooni ▴ 20

Hello. I'm trying to create a .tab file using a function called 'tidy_vcf' (see link).

tidy_vcf -v GWAS.vcf -o GWAS_sites.vcf -g GWAS_genotypes.vcf

However, when I run the above code, the following error continues to occur.

neither --sites (-s) or --thin (-t) were given. Using all VCF sites. This might take a while.
Traceback (most recent call last):
  File "C:\Users\ssu97\anaconda3\lib\runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\ssu97\anaconda3\lib\runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "C:\Users\ssu97\anaconda3\Scripts\tidy_vcf.exe\__main__.py", line 7, in <module>
  File "C:\Users\ssu97\anaconda3\lib\site-packages\tidy_vcf\tidy_vcf.py", line 179, in main
    parse_file(args.vcf, args.sites)
  File "C:\Users\ssu97\anaconda3\lib\site-packages\tidy_vcf\tidy_vcf.py", line 160, in parse_file
    info_headers = build_info(INFO, vcf_keys['info'], True)
  File "C:\Users\ssu97\anaconda3\lib\site-packages\tidy_vcf\tidy_vcf.py", line 62, in build_info
    values = [i[1] for i in info_pairs]
  File "C:\Users\ssu97\anaconda3\lib\site-packages\tidy_vcf\tidy_vcf.py", line 62, in <listcomp>
    values = [i[1] for i in info_pairs]
IndexError: list index out of range

What does this error mean? How can I solve this? Please help me. Thank you.

tidy_vcf manhattan vcf • 314 views

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