Stranger

Annotates output files from ExpansionHunter and TRGT with the pathologic implications of the repeat sizes.

Installation

Stranger uses the uv project manager. It is very quick and lightweight - see the uv installation instructions.

git clone github.com/clinical-genomics/stranger cd stranger uv pip install --editable .

Usage

``` uv run 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: $HOME/ stranger/stranger/resources/vari antcataloggrch37.json] -i, --family_id TEXT -t, --trgt File was produced with TRGT --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. ExpansionHunter 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 pathogenicity for the repeat number. The intervals that comes with the package are manually collected from the literature since there is no single source where this information can be collected.

You can find a demo repeat definitions json file that comes with Stranger here. It is based on the ExpansionHunter variant catalog, but extended with a few disease locus relevant keys: It is advisable to use an up to date file, perhaps based on a curated public repostitory such as STRchive or STRipy. The ones we use in our routine pipelines can be found at our Reference-files repository and include our literature curation.

| Column/Key | Content/Value | |-----------------|-------------------------------------------------------------------------------------------------| | HGNCID | HGNC identifier for the repeat or most associated gene. | | HGNCSYMBOL | HGNC symbol for the repeat or most associated gene. | | REPID | ExpansionHunter repeat ID. | | RU | Basic repeat unit, as seen in ExpansionHunter. Unused. | | DisplayRU | Repeat unit, as clinicians are used to see it. | | NormalMax | (#copies) Longest repeat expected for normal individual; higher are marked pre- or full-mutation | | PathologicMin | (#copies) Shortest repeat expected for pathology. This and higher is annotated as full-mutation. | | Disease | Associated disease. | | InheritanceMode | Mode of inheritance "AR", "AD", "XR" etc | | Source | Reference literature resource type, eg GeneReviews or PubMed | | SourceId | PMID or GeneReviews book ID for references | | TRID | Trgt repeat ID if not same as REPID | | PathologicStruc | Array of index for pathogenic motif |

Other fields accepted by ExpansionHunter are also encouraged.

Stranger can also read a legacy .tsv format file, structured like a Scout gene panel, with STR specific columns. The column names and keys correspond, but if in any kind of doubt, please read the code or use the json version.

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 #.

It is also possible to use an ExpansionHunter variant catalog json file with corresponding keys added. E.g. [ { "VariantType": "Repeat", "LocusId": "ATXN2", "LocusStructure": "(GCT)*", "ReferenceRegion": "chr12:112036753-112036822", "Disease": "SCA2", "NormalMax": 31, "PathologicMin": 39 }, { "VariantType": "Repeat", "LocusId": "PABPN1", "LocusStructure": "(GCG)*", "ReferenceRegion": "chr14:23790681-23790699", "Disease": "OPMD", "NormalMax": 6, "PathologicMin": 9 } ]

Such files are also provided with the distribution. PRs with updates are much appreciated.

Output

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

```

INFO=

4 3076603 . C , . PASS END=3076660;REF=19;RL=57;RU=CAG;VARID=HTT;REPID=HTT;STR_STATUS=normal,normal ```

TRGT mode

The flag --trgt will instruct Stranger to accept TRGT style VCFs. In particular, motif copy numbers are parsed from the GT.MC field and motifs listed in the PathologicStruc entry of the reference catalog: JSON { "VariantType": "Repeat", "LocusId": "RAPGEF2", "HGNCId": 16854, "InheritanceMode": "AD", "DisplayRU": "TTTCA", "SourceDisplay": "Ishiura et al (2018) Nature Genetics 50 581-90", "Source": "PubMed", "SourceId": "29507423", "LocusStructure": "(TTTTA)*(TTTCA)*(TTTTA)*", "ReferenceRegion": [ "4:160263679-160263703", "4:160263704-160263708", "4:160263709-160263768" ], "VariantType": [ "Repeat", "Repeat", "Repeat" ], "VariantId": [ "RAPGEF2_TTTTA_5P", "RAPGEF2", "RAPGEF2_TTTTA_3P" ], "PathologicRegion": "4:160263704-160263708", "PathologicStruc": [1], "Disease": "FAME7", "NormalMax": 1, "PathologicMin": 10 }, and ```VCF ...

FORMAT=

... 4 160263680 . TTTATTTTATTTTATTTTATTTTATATTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATT . 0 . TRID=FAME7RAPGEF2;END=160263770;MOTIFS=TTTTA,TTTCA;STRUC=(TTTTA)n(TTTCA)n(TTTTA)n;STRSTATUS=fullmutation;STRNORMALMAX=1;STRPATHOLOGICMIN=10;RankScore=internalid3:30;HGNCId=16854;InheritanceMode=AD;DisplayRU=TTTCA;SourceDisplay=Ishiura et al (2018) Nature Genetics 50 581-90;Source=PubMed;SourceId=29507423;Disease=FAME7 GT:AL:ALLR:SD:MC:MS:AP:AM 0/0:91,91:85-98,91-91:21,20:180,180:0(0-89)1(89-89)0(89-89),0(0-89)1(89-89)0(89-89):0.956044,0.956044:.,. 0/0:91,91:85-98,91-91:21,20:180,180:0(0-89)1(89-89)0(89-89),0(0-89)1(89-89)0(89-89):0.956044,0.956044:.,. 0/0:91,91:85-98,91-91:21,20:180,180:0(0-89)1(89-89)0(89-89),0(0-89)1(89-89)_0(89-89):0.956044,0.956044:.,. ... ```