Changes

From Genome Analysis Wiki
Jump to navigationJump to search

GotCloud: Filters (view source)

Revision as of 21:12, 27 August 2013

326 bytes added ,  21:12, 27 August 2013
no edit summary
Line 15: Line 15:  
| q || pred-scaled quality score || QUAL < FILTER_MIN_QUAL > 0 || 5
 
| q || pred-scaled quality score || QUAL < FILTER_MIN_QUAL > 0 || 5
 
|-
 
|-
−
| INDEL || || winIndel > 0 || 5
+
| INDEL || || FILTER_WIN_INDEL > 0 || 5
−
|-
  −
| FFRQ || || winFFRQ, maxFFRQ both > 0 || 0
   
|-
 
|-
 
| m || Root Mean Squared Mapping Quality || INFO:MQ < FILTER_MIN_MQ > 0 || 20
 
| m || Root Mean Squared Mapping Quality || INFO:MQ < FILTER_MIN_MQ > 0 || 20
Line 27: Line 25:  
| ns || Number of Samples With Coverage || INFO:NS < (FILTER_MIN_NS or FILTER_MIN_NS_FRAC * #samples) > 0 || .5*#samples
 
| ns || Number of Samples With Coverage || INFO:NS < (FILTER_MIN_NS or FILTER_MIN_NS_FRAC * #samples) > 0 || .5*#samples
 
|-
 
|-
−
| AB || Allele Balance in Heterozygotes || INFO:AB > FILTER_MAX_ABL/100. < 100 || 70,65
+
| AB || Allele Balance in Heterozygotes || INFO:AB > FILTER_MAX_ABL/100. < 1 || 70,65
 +
|-
 +
| STR || Strand Bias Pearson's Correlation || INFO:STR > FILTER_MAX_STR/100. < 1 || 20,10
 +
|-
 +
| str || Strand Bias Pearson's Correlation || INFO:STR < FILTER_MIN_STR/100. > -1 || -20,-10
 +
|-
 +
| stz ||Strand Bias z-score || INFO:STZ < FILTER_MIN_STZ > INT_MIN || -5,-10
 +
|-
 +
| STZ ||Strand Bias z-score || INFO:STZ > FILTER_MAX_STZ < INT_MAX || 5,10
 +
|-
 +
| fic || INFO:FIC < FILTER_MIN_FIC/100. > INT_MIN || -20,-10
 +
|-
 +
| CBR || Cycle Bias Peason's correlation || INFO:CBR > FILTER_MAX_CBR/100. < 1 || 20,10
 +
|-
 +
| LQR || INFO:LQR > FILTER_MAX_LQR/100. < 1 || 30,20
 +
|-
 +
| AOI || Alternate allele inflation score || INFO:AOI > FILTER_MAX_AOI < INT_MAX || 5
 +
|-
 +
| MQ0_ || Fraction of bases with mapQ=0 || INFO:MQ0 > FILTER_MAX_MQ0/100. < 1 || 10
 +
|-
 +
| IOR || Ratio of base-quality inflation || INFO:IOR || FILTER_MAX_IOR/100. < INT_MAX/100. || off
 +
|-
 +
| AOZ || Alternate allele quality z-score || INFO:AOZ > FILTER_MAX_AOZ < INT_MAX || off
 +
|-
 +
 
 +
 
 +
| FFRQ || || winFFRQ, maxFFRQ both > 0 || 0
 
|-
 
|-
 
| STP || INFO:STP || maxSTP || < INT_MAX ||  
 
| STP || INFO:STP || maxSTP || < INT_MAX ||  
Line 34: Line 58:  
|-
 
|-
 
| ttt || INFO:TTT || minTTT || > INT_MIN ||
 
| ttt || INFO:TTT || minTTT || > INT_MIN ||
−
|-
  −
| STR || INFO:STR || maxSTR/100. || < 100 || 20,10
  −
|-
  −
| str || INFO:STR || minSTR/100. || > -100 || -20,-10
   
|-
 
|-
 
| LQZ || INFO:LQZ || maxLQZ || < INT_MAX ||  
 
| LQZ || INFO:LQZ || maxLQZ || < INT_MAX ||  
−
|-
  −
| stz || INFO:STZ || minSTZ || > INT_MIN || -5,-10
  −
|-
  −
| STZ || INFO:STZ || maxSTZ || < INT_MAX || 5,10
   
|-
 
|-
 
| lqz || INFO:LQZ || minLQZ || > INT_MIN ||  
 
| lqz || INFO:LQZ || minLQZ || > INT_MIN ||  
Line 51: Line 67:  
| rbz || INFO:RBZ || minRBZ || > INT_MIN ||  
 
| rbz || INFO:RBZ || minRBZ || > INT_MIN ||  
 
|-
 
|-
−
| CBZ || INFO:CBZ || maxCBZ || < INT_MAX ||  
+
| CBZ || Cycle Bias z-score || INFO:CBZ > maxCBZ < INT_MAX ||  
−
|-
  −
| CBR || INFO:CBR || maxCBR/100. || < 100 || 20,10
   
|-
 
|-
 
| cbr || INFO:CBR || minCBR/100. || > -100 ||  
 
| cbr || INFO:CBR || minCBR/100. || > -100 ||  
Line 68: Line 82:  
|-
 
|-
 
| ior || INFO:IOR || minIOR/100. || > INT_MIN ||  
 
| ior || INFO:IOR || minIOR/100. || > INT_MIN ||  
−
|-
  −
| IOR || INFO:IOR || maxIOR/100. ||FILTER_MAX_IOR < INT_MAX || off
  −
|-
  −
| AOZ || INFO:AOZ || maxAOZ || FILTER_MAX_AOZ < INT_MAX || off
  −
|-
  −
| AOI || INFO:AOI > FILTER_MAX_AOI < INT_MAX || 5
  −
|-
  −
| MQ0_ || INFO:MQ0 || maxMQ0/100. || < 100 || 10
   
|-
 
|-
 
| MQ10_ || INFO:MQ10 || maxMQ10/100. || < 100 || off
 
| MQ10_ || INFO:MQ10 || maxMQ10/100. || < 100 || off
 
|-
 
|-
 
| MQ20_ || INFO:MQ20 || maxMQ20/100. || < 100 || off
 
| MQ20_ || INFO:MQ20 || maxMQ20/100. || < 100 || off
−
|-
  −
| fic || INFO:FIC || minFIC/100. || > INT_MIN || -20,-10
  −
|-
  −
| LQR || INFO:LQR || maxLQR/100. || < 100 || 30,20
   
|-
 
|-
 
| ABE || INFO:ABE || maxABE/100. || < 100 ||  
 
| ABE || INFO:ABE || maxABE/100. || < 100 ||  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/8417"

Navigation menu