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= 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 ==
{|border="1" cellspacing="0" cellpadding="2"
! Filter Prefix !! Filter Description !! Filter if !! Default Value
|-
| q || pred-scaled quality score || QUAL < FILTER_MIN_QUAL > 0 || 5
|-
| INDEL || || winIndel > 0 || 5
|-
| FFRQ || || winFFRQ, maxFFRQ both > 0 || 0
|-
| 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 > maxAB/100. < 100 ||
|-
| STP || INFO:STP || maxSTP || < INT_MAX ||
|-
| TTT || INFO:TTT || maxTTT || < INT_MAX ||
|-
| ttt || INFO:TTT || minTTT || > INT_MIN ||
|-
| STR || INFO:STR || maxSTR/100. || < 100 ||
|-
| str || INFO:STR || minSTR/100. || > -100 ||
|-
| LQZ || INFO:LQZ || maxLQZ || < INT_MAX ||
|-
| stz || INFO:STZ || minSTZ || > INT_MIN ||
|-
| STZ || INFO:STZ || maxSTZ || < INT_MAX ||
|-
| lqz || INFO:LQZ || minLQZ || > INT_MIN ||
|-
| RBZ || INFO:RBZ || maxRBZ || < INT_MAX ||
|-
| rbz || INFO:RBZ || minRBZ || > INT_MIN ||
|-
| CBZ || INFO:CBZ || maxCBZ || < INT_MAX ||
|-
| CBR || INFO:CBR || maxCBR/100. || < 100 ||
|-
| 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 ||
|-
| IOR || INFO:IOR || maxIOR/100. || < INT_MAX ||
|-
| AOZ || INFO:AOZ || maxAOZ || < INT_MAX ||
|-
| AOI || INFO:AOI || maxAOI || < INT_MAX ||
|-
| MQ0_ || INFO:MQ0 || maxMQ0/100. || < 100 ||
|-
| MQ10_ || INFO:MQ10 || maxMQ10/100. || < 100 ||
|-
| MQ20_ || INFO:MQ20 || maxMQ20/100. || < 100 ||
|-
| fic || INFO:FIC || minFIC/100. || > INT_MIN ||
|-
| LQR || INFO:LQR || maxLQR/100. || < 100 ||
|-
| 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 ||
|}
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 ==
{|border="1" cellspacing="0" cellpadding="2"
! Filter Prefix !! Filter Description !! Filter if !! Default Value
|-
| q || pred-scaled quality score || QUAL < FILTER_MIN_QUAL > 0 || 5
|-
| INDEL || || winIndel > 0 || 5
|-
| FFRQ || || winFFRQ, maxFFRQ both > 0 || 0
|-
| 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 > maxAB/100. < 100 ||
|-
| STP || INFO:STP || maxSTP || < INT_MAX ||
|-
| TTT || INFO:TTT || maxTTT || < INT_MAX ||
|-
| ttt || INFO:TTT || minTTT || > INT_MIN ||
|-
| STR || INFO:STR || maxSTR/100. || < 100 ||
|-
| str || INFO:STR || minSTR/100. || > -100 ||
|-
| LQZ || INFO:LQZ || maxLQZ || < INT_MAX ||
|-
| stz || INFO:STZ || minSTZ || > INT_MIN ||
|-
| STZ || INFO:STZ || maxSTZ || < INT_MAX ||
|-
| lqz || INFO:LQZ || minLQZ || > INT_MIN ||
|-
| RBZ || INFO:RBZ || maxRBZ || < INT_MAX ||
|-
| rbz || INFO:RBZ || minRBZ || > INT_MIN ||
|-
| CBZ || INFO:CBZ || maxCBZ || < INT_MAX ||
|-
| CBR || INFO:CBR || maxCBR/100. || < 100 ||
|-
| 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 ||
|-
| IOR || INFO:IOR || maxIOR/100. || < INT_MAX ||
|-
| AOZ || INFO:AOZ || maxAOZ || < INT_MAX ||
|-
| AOI || INFO:AOI || maxAOI || < INT_MAX ||
|-
| MQ0_ || INFO:MQ0 || maxMQ0/100. || < 100 ||
|-
| MQ10_ || INFO:MQ10 || maxMQ10/100. || < 100 ||
|-
| MQ20_ || INFO:MQ20 || maxMQ20/100. || < 100 ||
|-
| fic || INFO:FIC || minFIC/100. || > INT_MIN ||
|-
| LQR || INFO:LQR || maxLQR/100. || < 100 ||
|-
| 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 ||
|}
