tidy_vcf function
0
0
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
ADD COMMENT

Login before adding your answer.

Traffic: 1262 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6