Output Files ============= The :py:mod:`genipe` pipeline generates output files for each of the autosomal chromosomes (from 1 to 22). To get a description of those file, refer to the :ref:`genipe-tut-output-files` section of the tutorial. In summary, here is the structure of the output files. Again, refer to the :ref:`genipe-tut-output-files` section of the tutorial for more information. .. code-block:: text genipe/ │ ├── chr1/ │ ├── chr1.1_5000000.impute2 │ ├── chr1.1_5000000.impute2_info │ ├── chr1.1_5000000.impute2_info_by_sample │ ├── chr1.1_5000000.impute2_summary │ ├── chr1.1_5000000.impute2_warnings │ ├── ... │ ├── chr1.final.bed │ ├── chr1.final.bim │ ├── chr1.final.fam │ ├── chr1.final.log │ ├── chr1.final.phased.haps │ ├── chr1.final.phased.ind.me │ ├── chr1.final.phased.ind.mm │ ├── chr1.final.phased.log │ ├── chr1.final.phased.sample │ ├── chr1.final.phased.snp.me │ ├── chr1.final.phased.snp.mm │ ├── ... │ │ │ └── final_impute2/ │ ├── chr1.imputed.alleles │ ├── chr1.imputed.completion_rates │ ├── chr1.imputed.good_sites │ ├── chr1.imputed.impute2.gz │ ├── chr1.imputed.impute2_info │ ├── chr1.imputed.imputed_sites │ ├── chr1.imputed.log │ ├── chr1.imputed.maf │ ├── chr1.imputed.map │ └── chr1.imputed.sample │ ├── .../ │ ├── chromosome_lengths.txt ├── exclusion_summary.txt ├── frequency_pie.pdf ├── genipe.log ├── markers_to_exclude.txt ├── markers_to_flip.txt │ ├── missing │ ├── missing.imiss │ ├── missing.lmiss │ └── missing.log │ ├── report │ ├── frequency_pie.pdf │ ├── Makefile │ ├── references.bib │ ├── references.bst │ └── report.tex │ └── tasks.db