<commit_before>molgenis-imputeute
===============

Rapid generation of genetic imputation scripts for grid/cluster/local environments


## About 
molgenis-impute is a tool for rapid generation and submission of scripts that perform genetic imputation. The generated scripts contain all rigorous quality control checks, data chunking, error handling and reporting. The tool is designed to be simple and straight-forward, for researchers that want to do imputation **now**, without limiting the available options of imputation tools.

molgenis-impute performs three main actions:
* liftover (from hg18 to hg19 genomic reference)
* phasing of a study panel
* imputation

## Requirements
molgenis-impute runs in any 64-bit x86 linux distribution and it requires the following tools:
* wget (or curl)
* tar
* unzip
* g++
* python 2.7

Also note that imputation reference panels can take tens of GBs of disk space 

## Setup 
Initially, run the following to download all necessary tools for imputation:
```
python molgenis-impute.py --dl_tools```

Then download a reference panel of your choice. To list all available reference panels for downloading, run: 
```
python molgenis-impute.py --list```

To download a reference panel. Run:
```
python molgenis-impute.py --dl_reference < NAME >```

where < NAME > is the name of the reference panel as provided by the --list option.

## Imputation study panel<commit_msg>Fixed format<commit_after>molgenis-imputeute
===============

Rapid generation of genetic imputation scripts for grid/cluster/local environments


## About 
molgenis-impute is a tool for rapid generation and submission of scripts that perform genetic imputation. The generated scripts contain all rigorous quality control checks, data chunking, error handling and reporting. The tool is designed to be simple and straight-forward, for researchers that want to do imputation **now**, without limiting the available options of imputation tools.

molgenis-impute performs three main actions:
* liftover (from hg18 to hg19 genomic reference)
* phasing of a study panel
* imputation

## Requirements
molgenis-impute runs in any 64-bit x86 linux distribution and it requires the following tools:
* wget (or curl)
* tar
* unzip
* g++
* python 2.7

Also note that imputation reference panels can take tens of GBs of disk space 

## Setup 
Initially, run the following to download all necessary tools for imputation:
```
python molgenis-impute.py --dl_tools
```

Then download a reference panel of your choice. To list all available reference panels for downloading, run: 
```
python molgenis-impute.py --list
```

To download a reference panel. Run:
```
python molgenis-impute.py --dl_reference < NAME >
```

where < NAME > is the name of the reference panel as provided by the --list option.

## Imputation study panel
{'fraction_non_alphanumeric': 0.075177304964539, 'fraction_numerical': 0.0070921985815602835, 'mean_word_length': 4.653306613226453, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 8, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4242039', 'n_tokens_mistral': 801, 'n_tokens_neox': 728, 'n_words': 368}