User:Lindenb/Notebook/UMR915/20101012

20101011        Top        20101013       

• Polyphen2 has been updated for all transcripts: http://genetics.bwh.harvard.edu/pph2/bgi.shtml
• Strikes. Working at home.

Belgium

generating input for PPH2

  jrunscript -f jeter.js > jeter.polyphen.txt
  
  wc jeter.polyphen.txt
  62548

submitted both batch for hg18 at 09H45. Waiting... http://genetics.bwh.harvard.edu/cgi-bin/ggi/ggi2.cgi end at ~15H00

 diff HumDiv.txt HumVar.txt | wc
 0

Results for HumDiv

 ## Totals:
 ##   lines input           62548
 ##   lines skipped             0
 ##   alleles annotated     63107
 ##     missense              551
 ##     nonsense                3
 ##     coding-synon          369
 ##     intron              60567
 ##     utr-3                1473
 ##     utr-5                 144

Results for HumVar

 ## Totals:
 ##   lines input           62548
 ##   lines skipped             0
 ##   alleles annotated     63107
 ##     missense              551
 ##     nonsense                3
 ##     coding-synon          369
 ##     intron              60567
 ##     utr-3                1473
 ##     utr-5                 144

Huuu??? Using file named "SNPs" : No diff beteen HumDiv and HumVar ??? but XML files say ok with params

 <WEKA Class="deleterious"
       FDR="0.182"
       FPR="0.262"
       Modelfile="HumVar.UniRef100.NBd.f11.model"
       Prediction="possibly damaging"
       Score="0.513"
       TPR="0.806" />

and

 <WEKA Class="deleterious"
       FDR="0.211"
       FPR="0.111"
       Modelfile="HumDiv.UniRef100.NBd.f11.model"
       Prediction="possibly damaging"
       Score="0.654"
       TPR="0.828" />

But using filesn "Short"

diff HumVarChrXXX.txt HumDivChrXXX.txt | wc
840