GIAB  Mee(ng    

Elizabeth  Hénaff  Chris  Mason  

 NIST  

Aug  26th,  2015    

Casacuberta and Santiago 2003

JITTERBUG      Hénaff  et  al  2015  –  BMC  Genomics  (in  press)  

insertion site

properly mapped core reads support heterozygous insertion

discordant read pairspredict a TE insertion

softclipped reads predict exact breakpoint

anchor TE mate

predicted insertion interval

anchorTE mate

fwd cluster

rev cluster

ref support

supporting fwd reads

supporting rev reads

length

span

softclipped support

83%  of  variable  loci  respect  possible  inherited  genotypes    17%  are  either  FN  or  FP  or  mis-­‐called  allelic  frequency    11  inser(ons  are  poten(ally  novel  to  child  

Future  Perspec(ves    -­‐  Run  on  full  coverage  trios  (so  far  ran  on  90X  bams)      -­‐  Use  similar  approach  to  T/N  to  call  FN  in  related  datasets  

-­‐  Further  study  inheritance  pa\erns  (by  chromosome)      

THANKS!!      CRG:  Stephan  Ossowski  +  lab    Josep  Casacuberta    Weill  Cornell:  Chris  Mason  +  lab