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Update README...
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link to scout, and an almost up to date VCF header..
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dnil authored Dec 13, 2019
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Expand Up @@ -62,7 +62,7 @@ There is a repeat definitions file that comes with Stranger in `stranger/resourc
| 14203 | JPH3 | JPH3 | CTG | 28 | 40 | HDL2 |
| 644 | AR | AR | CAG | 35 | 38 | SBMA |

The file is structured like a SCOUT (https://github.com/Clinical-Genomics/scout) gene panel, with STR specific columns.
The file is structured like a [Scout](https://github.com/Clinical-Genomics/scout) gene panel, with STR specific columns.

| Column | Content |
| ------- | ------- |
Expand Down Expand Up @@ -101,6 +101,15 @@ It is also possible to use an ExpansionHunter variant catalog json file with cor
]
```

## Output

Output is by annotated VCF, with keys `STR_STATUS`, `NormalMax` and `PathologicMin`.

```
##INFO=<ID=STR_STATUS,Number=A,Type=String,Description="Repeat expansion status. Alternatives in [normal, pre_mutation, full_mutation]">
4 3076603 . C <STR17>,<STR18> . PASS END=3076660;REF=19;RL=57;RU=CAG;VARID=HTT;REPID=HTT;STR_STATUS=normal,normal
```

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

[travis-url]: https://travis-ci.com/moonso/stranger
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