Output

Create a new directory <feature name>_<run name> containing the following files:

Log file

Text, one file for each job chromosome??

 parameters

Feature annotation file

Tab separated text file containing the feature metadata for the feature_ids processed in the pipeline

Name: feature_metadata_<chr>.h5

 feature_id
 chromosome
 start
 end
 [ensembl_gene_id]
 [feature_strand]
 [gene_name]
 [superior_feature_id]

SNP metadata file

Tab separated text file containing the SNP metadata for the snp_id processed in the pipeline

Name: snp_metadata_<chr>.h5

snp_id 
chromosome 
position
assessed_allele

Results file

HDF5, one file for each chromosome

Name: qtl_results_(_Perm<PermRound>).h5

| feature_id
| + data [#fields, #SNP] {'snp_id', 'number_samples','beta','p_value '}

Aggregation of chromosome results in one file. Deal with permutations at the same step.