Issue with target genotype harmonization: MissingInputException when done with VCF as input

[Felicia648]

Hi everyone, I'm new to coding and Snakemake so I needed some help.
Unfortunately, I've encountered a problem when I tried the bash run.sh all_harmonize_target_genotypes step when trying to use VCF as input.

Following the documentation, my target_list configuration looks like this:

name    path    type
result37        /home/felicia/asian_result37/result37zip_chromosomes/result37_chr       samp_imp_vcf

I have tried using both .vcf and .vcf.gz file as input but both times, the error message below appears.

MissingInputException in rule harmonize_target_genotypes in file /home/felicia/prspipe/workflow/rules/genotype_harmonization.smk, line 29:
Missing input files for rule harmonize_target_genotypes:
    output: custom_input/result37/genotypes/chr1.bim, custom_input/result37/genotypes/chr1.bed, custom_input/result37/genotypes/chr1.fam
    wildcards: bbid=result37, chr=1
    affected files:
        /home/felicia/asian_result37/result37_chromosomes/result37_chr1.vcf

I'm not sure what went wrong or which input I am missing in this case, can anybody help me? Thanks!

[remomomo]

Hi,

Can you provide more details on your setup?

You should have 1 VCF file per chromosome in the folder /home/felicia/asian_result37/result37_chromosomes/