Difference between revisions of "GotCloud: Filters"

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| 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 ||  
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|-
 
|-
 
| 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 ||  
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|-
 
|-
 
| 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 ||  

Revision as of 21:12, 27 August 2013

GotCloud Filters

GotCloud uses multiple filters throughout the GotCloud Pipeline.

The primary filters applied are during the Variant Calling snpcall step.

There are two phases of filters:

  • Hard Filters
  • SVM Filters

Hard Filters

Filter Prefix Filter Description Filter if Default Value
q pred-scaled quality score QUAL < FILTER_MIN_QUAL > 0 5
INDEL FILTER_WIN_INDEL > 0 5
m Root Mean Squared Mapping Quality INFO:MQ < FILTER_MIN_MQ > 0 20
dp Total Depth at Site INFO:DP < #samples * FILTER_MIN_SAMPLE_DP > 0 #samples*1
DP Total Depth at Site INFO:DP > #samples * FILTER_MAX_SAMPLE_DP < INT_MAX #samples*1000
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. < 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
TTT INFO:TTT maxTTT < INT_MAX
ttt INFO:TTT minTTT > INT_MIN
LQZ INFO:LQZ maxLQZ < INT_MAX
lqz INFO:LQZ minLQZ > INT_MIN
RBZ INFO:RBZ maxRBZ < INT_MAX
rbz INFO:RBZ minRBZ > INT_MIN
CBZ Cycle Bias z-score INFO:CBZ > maxCBZ < INT_MAX
cbr INFO:CBR minCBR/100. > -100
QBR INFO:QBR maxQBR/100. < 100
qbr INFO:QBR minQBR/100. > -100
CSR INFO:CSR maxCSR/100. < 100
csr INFO:CSR minCSR/100. > -100
IOZ INFO:IOZ maxIOZ < INT_MAX
ior INFO:IOR minIOR/100. > INT_MIN
MQ10_ INFO:MQ10 maxMQ10/100. < 100 off
MQ20_ INFO:MQ20 maxMQ20/100. < 100 off
ABE INFO:ABE maxABE/100. < 100
abe INFO:ABE minABE/100. > -100
MBR INFO:MBR maxMBR/100. < 100
mbr INFO:MBR minMBR/100. > -100
ABZ INFO:ABZ maxABZ < INT_MAX
abz INFO:ABZ minABZ > INT_MIN
BCS INFO:BCS maxBCS < INT_MAX
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