Commits for angie

v281_preview2 to v281_base (2013-03-19 to 2013-03-25) v281

• Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
  http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
  dbNSFP2.0 contains precomputed predictions from a variety of tools of the
  effects of all possible missense variants on protein-coding Gencode rel 9
  (Ens 64) transcripts. For example, it contains scores and predictions
  from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
  LRT), as well as GERP scores at CDS positions and associated domain
  information from InterPro and IDs from UniProt. Each subset is
  extracted into a bigBed or bigWig file so that users of the Variant
  Annotation Integrator will be able to apply one or more of these
  prediction methods to their variants.
  refs #6152
  
  • src/hg/lib/dbNsfpInterPro.as - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/dbNsfpLrt.as - lines changed 21, context: html, text, full: html, text
  • src/hg/lib/dbNsfpMutationAssessor.as - lines changed 18, context: html, text, full: html, text
  • src/hg/lib/dbNsfpMutationTaster.as - lines changed 18, context: html, text, full: html, text
  • src/hg/lib/dbNsfpPolyPhen2.as - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/dbNsfpSeqChange.as - lines changed 21, context: html, text, full: html, text
  • src/hg/lib/dbNsfpSift.as - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/dbNsfpUniProt.as - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 68, context: html, text, full: html, text
  • src/hg/utils/dbNsfpToBed.pl - lines changed 379, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/mergeSortedBed3Plus.pl - lines changed 64, context: html, text, full: html, text
• Correcting the /hive path for dbNSFP2.0
  • src/hg/makeDb/doc/hg19.txt - lines changed 2, context: html, text, full: html, text