This PR adds a rule in the preprocessing with qc pipeline that checks for individual missingness.
And excludes samples over certain threshold.
Two new rules are added to the snakemake pipeline rule qc_indmiss and process_individual_missingness the first one uses bcftools to generate the stats and the second one uses the new process-individual-missingness cmd in the preprocessing tool that actually finds the samples over the threshold and writes them to the filter_samples directory.
What
This PR adds a rule in the preprocessing with qc pipeline that checks for individual missingness. And excludes samples over certain threshold.
Two new rules are added to the snakemake pipeline rule
qc_indmissandprocess_individual_missingnessthe first one uses bcftools to generate the stats and the second one uses the newprocess-individual-missingnesscmd in the preprocessing tool that actually finds the samples over the threshold and writes them to the filter_samples directory.