Output Files

The 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 Output files section of the tutorial.

In summary, here is the structure of the output files. Again, refer to the Output files section of the tutorial for more information.

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