用str变量注释vcf文件
stranger的Python项目详细描述
陌生人
用重复大小的病理含义注释ExpansionHunter的输出文件。
安装
git clone github.com/moonso/stranger
cd stranger
pip install --editable .
用法
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.
重复定义
如前所述，在expansion hunter中调用repeats。expansion hunter将注释在每个个体的bam文件中看到重复的次数，以及变体的重复id。
陌生人会为重复数标注致病性水平。包附带的间隔是从文献中手动收集的，因为没有可以收集此信息的来源。
在stranger/resources/repeatexpansionsloci.tsv中有一个陌生人附带的重复定义文件。这是一个TSV格式的文件，格式如下：
| 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 |
该文件的结构类似于scout基因面板，具有str特定的列。
| 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. |
默认情况下，将使用分发后的文件，但用户可以创建自己的文件。
标题行前面应该有一个#。
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