瀏覽代碼

Update: README

master
YaqingLiu 4 年之前
父節點
當前提交
01d17edd41
共有 1 個檔案被更改,包括 18 行新增11 行删除
  1. +18
    -11
      README.md

+ 18
- 11
README.md 查看文件

### Variant Calling ### Variant Calling
This APP developed for germline and somatic short variant discovery (SNVs + Indels). This APP developed for germline and somatic short variant discovery (SNVs + Indels).


**Supported Callers**
>**Accepted Data**
* TN matched WES for somatic variant calling
* TN matched WGS for somatic variant calling
* Normal-only WES for germline variant calling
* Normal-only WGS for germline variant calling

The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).


>**Supported Callers**


* The fields corresponding to these callers include `haplotyper`, `tnseq`, `tnscope`, `varscan`.
* All callers are <u>**not activated by default**</u>, which means the default setting is `false`. * All callers are <u>**not activated by default**</u>, which means the default setting is `false`.
* You need to manually set the caller to `true` in the submitted sample.csv. * You need to manually set the caller to `true` in the submitted sample.csv.
* The fields corresponding to these callers include `haplotyper`, `tnseq`, `tnscope`, `varscan`.


<u>***Germline***</u> <u>***Germline***</u>
* Haplotyper * Haplotyper
* TNseq (TNhaplotyper2) * TNseq (TNhaplotyper2)
* TNscope * TNscope
* VarScan * VarScan
* TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated)


**Accepted Data**
* TN matched WES for somatic variant calling
* TN matched WGS for somatic variant calling
* Normal-only WES for germline variant calling
* Normal-only WGS for germline variant calling


The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).
>**Annotation Tools**
* The fields corresponding to two tools include `annovar`, `vep`.
* All tools are <u>**not activated by default**</u>, which means the default setting is `false`.
* You need to manually set the caller to `true` in the submitted sample.csv.


### New Releases ### New Releases
* TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2. * TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.




**Please carefully check** **Please carefully check**
* the reference genome you want to use is hg38.
* the reference genome you want to use is hg38 or hg19.
* bed file. * bed file.
* the caller you want to use. * the caller you want to use.
* PoN VCFs for TNseq and TNscope is supported, but are need to be generated in advance. * PoN VCFs for TNseq and TNscope is supported, but are need to be generated in advance.
* interval padding is default 0, and you can change it.
* interval padding is default 0, and you can change it.
* the annotation tool is ANNOVAR or VEP.

Loading…
取消
儲存