stmp3 | A third , more modest but less broken version of stmp

stmp3 is a Python library. stmp3 has no bugs, it has no vulnerabilities and it has low support. However stmp3 build file is not available. You can download it from GitHub.

A third, more modest but less broken version of stmp. usage: python analysis_pipeline_master_script.py argument_configs.tsv please refer to the file template.tsv for an explanation of potential arguments Example usage: NA12878. Using the sequencing data for NA12878, and an XLS generated by ingenuity for NA12878, run the pipeline. Go to the directory on sherlock: /scratch/PI/euan/common/udn/externalUdnData/NA12878. Adjust the file NA12878_analysis_run.tsv as needed then run python path/to/analysis_pipeline_master_script.py NA12878_analysis_run.tsv. This takes approximately 10 minutes to run, and will generate a merged xls and powerpoint. Design philosophies "currentWorking[vcf, xls etc]"--> in order to facilitate the. This script is the 2017 iteration of the pipeline sequence to medical pheontype (stmp). It has evolved from the goals outlined in stmp2. Whereas stmp aimed to implement all aspects of an annotation pipeline, from intfrastructure to algorithms stmp3 is more modest in its ambition. It leverages third party tools (vcfanno etc) wherever possible and aims to augment the insights and processes used by the genetic counseling team. The main script for this repository is analysis_pipeline_master_script.py. As the name implies, this pipeline aims to perform all aspects of analysis and processing of our sequencing data, from intial processing of bams, fastqs, and vcfs, to endpoint user motivated processing of excel sheets, powerpoint slides, and web based visualization Here are the stages of processing data in the pipeline goes through, and the associated file suffix that is added (where relevant). Note that file suffixes can be rendered in plain english by using the script "????.py". Part 0: check coherency of arguments--stub code, Currently not implemented. Part 1: calling. Stub for calling rtg. Currently not implemented.