Input Files

Multiple input files are required for genipe, including the initial genotypes and the reference files (for imputation). For a thorough description of these files, see the Input files section of the tutorial.

Here is a typical project directory structure. Again, refer to the Input files section of the tutorial for more information.

$HOME/genipe_tutorial/
│
├── 1000GP_Phase3/
│   ├── 1000GP_Phase3_chr1.hap.gz
│   ├── 1000GP_Phase3_chr2.hap.gz
│   ├── ...
│   ├── 1000GP_Phase3_chr1.legend.gz
│   ├── 1000GP_Phase3_chr2.legend.gz
│   ├── ...
│   ├── 1000GP_Phase3.sample
│   ├── genetic_map_chr1_combined_b37.txt
│   ├── genetic_map_chr2_combined_b37.txt
│   └── ...
│
├── bin/
│   ├── impute2
│   ├── plink
│   └── shapeit
│
├── data/
│   ├── hapmap_CEU_r23a_hg19.bed
│   ├── hapmap_CEU_r23a_hg19.bim
│   └── hapmap_CEU_r23a_hg19.fam
│
├── genipe_config.ini  # OPTIONAL (--use-drmaa, --drmaa-config)
│
├── hg19/
│   ├── hg19.fasta
│   └── hg19.fasta.fai
│
└── preamble.txt     # OPTIONAL (--use-drmaa, --preamble)