Changes

# Currently, GenomeSTRiP only allows calling large deletions, but duplicate calling pipeline is under way.

# Currently, GenomeSTRiP only allows calling large deletions, but duplicate calling pipeline is under way.

=== Why do we use GotCloud/GenomeSTRiP pipeline instead of directly using GenomeSTRiP itself? ===

=== Why do we use GotCloud/GenomeSTRiP pipeline? ===

# The main purpose of GotCloud pipelines is to provide a pipeline for users with limited knowledge and experience with high performance computing environment.  

# The main purpose of GotCloud pipelines is to provide a pipeline for users with limited knowledge and experience with high performance computing environment.

#* Although GenomeSTRiP provides a reasonably straightforward pipeline, it still requires a detailed understanding of GATK framework and the details of parameter.

#* GotCloud/GenomeSTRiP provide a simple interface consistent to alignment, SNP, and indel calling.

#* GotCloud aims to provide more simpler way to run these procedure

#* GenomeSTRiP itself also provides a straightforward pipeline to use as standalone software

# GotCloud supports a variety of cluster environment that is not currently supported by GenomeSTRiP

# GotCloud supports a variety of cluster environment that is not currently supported by GenomeSTRiP

#* GenomeSTRiP is designed based on a framework called Qscript, which provide a nice support for LSF cluster system, but it does not support many other cluster enviroments such as MOSIX or SLURM we use locally.

#* GenomeSTRiP is designed based on a framework called Qscript, which provide a nice support for LSF cluster system

#* GotCloud support many additional cluster environments such as MOSIX or SLURM we use locally at Michigan.

# GotCloud also provide a fault-tolerant solution for large-scale jobs.

# GotCloud also provide a fault-tolerant solution for large-scale jobs.

#* GotCloud automatically picks up jobs from the point where it failed. This allows easier and simpler run against potential technical glitches in the system.

#* GotCloud automatically picks up jobs from the point where it failed. This allows easier and simpler run against potential technical glitches in the system.