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Annotate VCF files with str variants

Project description

Stranger Build Status Coverage Status PyPI Version

Annotates output files from ExpansionHunter 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 #.

Project details


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