Update README.md

README.md

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-# comboSC-mut
+# comboSC-mut
+A pipeline for gene mutation identification from single-cell RNA-sequencing
+
+## 1. Introduction
+
+comboSC-mut is a pipeline based on [SCmut](https://github.com/nghiavtr/SCmut/projects)
+, which is used to provide more information for the selection of treatment stretegy in comboSC. SCmut is a novel and robust statistical method for cell-level somatic mutation detection from single-cell RNA-sequencing. SCmut requies RNA-sequencing data of single cells and bulk-cell DNA-sequencing (e.g whole exome sequencing - WES) of matched samples (tumor and normal). If the DNA-sequencing data are not available, the list of somatic mutations can be used.
+
+Software requirements for SCmut:
+
+SCmut
+Java 1.8 or higher
+
+R 3.2 or higher
+
+Samtools 1.3 or higher
+
+Picard 2.3 or higher
+
+VarScan 2.3.7 or higher
+
+GATKAnalysisTK 3.6 or higher
+
+## 2. Usage
+### 2.1 Create a file named "comboSC-para", containing the following parameters:fasta, dbsnp, known_Mills_indels, known_1000G_indels.
+
+#### example
+fasta="/home/zhouchi/pTuneos/database_backup/Fasta/human.fasta"
+dbsnp="/home/zhouchi/pTuneos/database_backup/VCF_annotation/dbsnp_138.hg38.vcf.gz"
+known_Mills_indels="/home/zhouchi/pTuneos/database_backup/VCF_annotation/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
+known_1000G_indels="/home/zhouchi/pTuneos/database_backup/VCF_annotation/1000G_phase1.indels.hg38.sites.vcf.gz"
+
+### 2.2 run code:
+`bash SCmut.R`
+
+