Update: README

README.md

@@ -1,11 +1,20 @@
 ### Variant Calling
 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`. 
 * 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>
 * Haplotyper
@@ -14,15 +23,12 @@ This APP developed for germline and somatic short variant discovery (SNVs + Inde
 * TNseq (TNhaplotyper2)
 * TNscope
 * 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-* TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated)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
 * TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
@@ -57,8 +63,9 @@ The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2,
 
 
 **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.
 * the caller you want to use.
 * 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.