Miad - Predixcan

[sagehen03]

• new susie method
• clean code
• clean up code
• clean up code
• back susie.scala
• clean up code - ancestry specific
• clean up code - ancestry specific
• add safe_remove function '
• add Finemap into susie branch
• change input in MakeFinemap.scala
• finemap
• update Finemap.scala
• update MakeFinemap.scala
• update Finemap.scala
• update MakeFinemap.scala
• create new finemap
• not importing some MemorySize, and Ec2.Strategy
• update finemap
• update finemap
• udpate finemap
• udpate finemap
• modify susie for finemap
• udpate finemap
• apt-get into yum
• apt-get into yum
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• *update .py
• update install-finemap.sh
• run without active conda environment
• run without active conda environment
• run without active conda environment
• run without active conda environment
• run without active conda environment
• add zstd in install-finemap.sh
• update makeFinemap.py
• update makeFinemap.py
• update run_finemap_pipeline.sh
• update run_finemap_pipeline.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• update install-finemap.sh
• change command for jq
• update command
• update command
• update command
• update command
• update command
• update command
• Final-clean
• Final-clean:premission to finemap
• Final-clean:premission update
• Final-clean:premission update
• Final-clean:premission update
• Final-clean:premission update+
• add parallel
• add parallel
• add parallel
• add parallel
• add parallel
• change command more filter on config
• update loading data
• update loading data
• prs first version
• install updated
• update makePRS
• makePRS udpated
• make aws transfer in makePRS.py
• make aws transfer in makePRS.py
• make aws transfer in makePRS.py
• make aws transfer in makePRS.py
• make aws transfer in makePRS.py
• update to dbSNP in makePRS.py
• update to dbSNP in makePRS.py
• update to dbSNP in makePRS.py
• update install-prs
• update install-prs
• parallel makePRS
• single chrom makePRS
• update parameters
• filter gwas
• filter gwas
• update combined result
• update combined result
• import re
• import re
• import re
• import re
• updated PRS for X and Y chrom
• updated PRS for X and Y chrom
• update ct
• update ct
• update ct
• as noted in prscsx method, sex is skipped
• update C+T methods
• update C+T methods
• update C+T methods
• update C+T methods
• update C+T methods
• update C+T methods
• update C+T methods
• predixcan method
• sPrediXcan
• sPrediXcan
• sPrediXcan
• sPrediXcan