NGSpeAnalysis is a pipeline based on open-source software capable of discovering high-quality variation and genotyping individual sample. The pipeline will use BWA, GATK, Picard, ANNOVAR and BEDTools to conduct analysis from alignment of pair ended short reads generated by Next Generation Sequencing machine to high quality variants genotype calling.
The pipeline also includes the steps for annotation and genotype calling for multiple samples. A shell script(used for Linux PC) and a PBS script (used for high performance computing environment) as well as the raw data of our pair-ended sequenced sample are available. Users could download and run a test by using the scripts and the sample data.
Users need to make sure that the file path in the script had been changed correctly according to your own computer's situation before running.