sv-call

README.md

@@ -1,15 +1,27 @@
 # snakeflow
+My NGS workflows based on snakemake
+
+**workflows include**:
+- RNA-seq (Salmon,hisat2)
+- ChIP-seq (MACS2)
+- ATAC-seq (MACS2)
+- CITE-seq (Antibody captured, 10X genomics)
+- Germline SNV calling (GATK, BCFtools)
+- Germline Structural Variant calling (Speedseq + svtools)
 
-### RNA-Seq and ChIP-seq workflow based on snakemake
 
 ## Dependency
+
 * python 3
   - numpy
   - pandas
   - snakemake
   - matplotlib
   - seaborn
   - gseapy
+  - macs2
+  - rseqc
+
 
 * hisat2, salmon
 * samtools, deeptools, bedtools
@@ -27,6 +39,10 @@
   - ChIPSeeker
   - EnsDb.Hsapiens.v86
 
+* cellranger
+* GATK (> 4.0)
+* Speedseq + svtools
+
 ## Installation
 
 ### Set up running environment. This config file will create a python 3.x env.

data/mouse.mm10.excl.bed

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