wgs_pipeline_on_hg19

whole human genome sequence alignment/mapping pipeline on hg19 reference genome

reference genome and public databases were downloaded from broadinstitute official ftp server

wget -m -N ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.8/hg19 # currently link is changed

gatk version used in this pipeline is 3.8-1-0-gf15c1c3ef

list of files:

• .gitignore
• bash_pipeline.sh - sample of script generated by wgs_pipeline_on_hg19.py
• CHANGELOG.md - list of changes as pipeline developed
• environment.yml - instructions for new conda environment
• README.md - this file
• sswgsap.py - old version of pipeline, old format
• wgs_pipeline_on_hg19.py - full version of pipeline, new format