stranger 0.4

Annotate VCF files with str variants

# Stranger [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-url]

Annotates output files from [ExpansionHunter][hunter] with the pathologic implications of the repeat sizes.

## Installation

```
git clone github.com/moonso/stranger
cd stranger
pip install --editable .
```

## Usage

```
stranger --help
Usage: stranger [OPTIONS] VCF

Annotate str variants with str status

Options:
-f, --repeats-file PATH Path to a file with repeat definitions. See
README for explanation [default: /Users/man
smagnusson/Projects/stranger/stranger/resour
ces/repeatexpansionsloci.tsv]
--version
--loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]
Set the level of log output. [default:
INFO]
--help Show this message and exit.

```


## Repeat definitions

The repeats are called with Expansion Hunter as mentioned earlier. Expansion Hunter will annotate the number of times that a repeat has been seen in the bam files of each individual and what repeat id the variant has.
Stranger will annotate the level of pathogenecity for the repeat number. The intervals that comes with the package are manually collected from the literature since there is no source where this information can be collected.
There is a repeat definitions file that comes with Stranger in `stranger/resources/repeatexpansionsloci.tsv`. This is a tsv formated file on the following format:

| hgnc_id | hgnc_symbol | repid | ru | normal_max | pathologic_min | disease |
| ------- | ------- | ------- | ------- | ------- | ------- | ------- |
| 10548 | ATXN1 | ATXN1 | CAG | 35 | 45 | SCA1 |
| 10555 | ATXN2 | ATXN2 | CAG | 31 | 39 | SCA2 |
| 7106 | ATXN3 | ATXN3 | CAG | 44 | 60 | SCA3 |
| 1388 | CACNA1A | CACNA1A | CAG | 18 | 20 | SCA6 |
| 10560 | ATXN7 | ATXN7 | CAG | 19 | 37 | SCA7 |
| 10561 | ATXN8OS | ATXN8OS | CAG | 50 | 80 | SCA8 |
| 10549 | ATXN10 | ATXN10 | ATTCT | 32 | 800 | SCA10 |
| 9305 | PPP2R2B | PPP2R2B | CAG | 35 | 49 | SCA12 |
| 11588 | TBP | TBP | CAG | 31 | 49 | SCA17 |
| 3951 | FXN | FXN | CAG | 35 | 51 | FRDA |
| 4851 | HTT | HTT | CCG | 36 | 37 | Huntington |
| 3775 | FMR1 | FMR1 | CGG | 65 | 200 | FragileX |
| 3776 | AFF2 | AFF2 | CCG | 25 | 200 | FRAXE |
| 13164 | CNBP | CNBP | CCTG | 30 | 75 | DM2 |
| 2933 | DMPK | DMPK | CAG | 37 | 50 | DM1 |
| 3033 | ATN1 | ATN1 | CAG | 34 | 49 | DRPLA |
| 15911 | NOP56 | NOP56 | GGCCTG | 14 | 650 | SCA36 |
| 28337 | C9ORF72 | C9ORF72 | GGCCCC | 25 | 40 | FTDALS1 |
| 8565 | PABPN1 | PABPN1 | GCG | 6 | 10 | OPMD |
| 2482 | CSTB | CSTB | CGCGGGGCGGGG | 3 | 30 | EPM1 |
| 1541 | CBL | CBL | CGG | 79 | 100 | FRAX11B |
| 14203 | JPH3 | JPH3 | CTG | 28 | 40 | HDL2 |
| 644 | AR | AR | CAG | 35 | 38 | SBMA |

The file is structured like a SCOUT gene panel, with STR specific columns.

| Column | Content |
| ------- | ------- |
| HGNC_ID | HGNC identifier for the repeat or most associated gene. |
| HGNC_SYMBOL |HGNC symbol for the repeat or most associated gene. |
| REPID | ExpansionHunter repeat ID. |
| RU | Basic repeat unit, as seen in ExpansionHunter. Unused. |
| Normal_Max | (#copies) Longest repeat expected for normal individual; higher are marked pre- or full-mutation |
| Pathologic_Min | (#copies) Shortest repeat expected for pathology. This and higher is annotated as full-mutation. |
| Disease | Associated disease. |

As a default the file that follows the distribution is used but the users can create their own file.
Header line(s) should be preceded with a `#`.


[hunter]: https://github.com/Illumina/ExpansionHunter

[travis-url]: https://travis-ci.com/moonso/stranger
[travis-image]: https://travis-ci.com/moonso/stranger.svg?branch=master

[coveralls-url]: https://coveralls.io/github/moonso/stranger
[coveralls-image]: https://coveralls.io/repos/github/moonso/stranger/badge.svg?branch=master