GotCloud: Filters
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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 | 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 > FILTER_MAX_ABL/100. < 100 | 70,65 | |
| STP | INFO:STP | maxSTP | < INT_MAX | |
| TTT | INFO:TTT | maxTTT | < INT_MAX | |
| 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 | |
| stz | INFO:STZ | minSTZ | > INT_MIN | -5,-10 |
| STZ | INFO:STZ | maxSTZ | < INT_MAX | 5,10 |
| 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 | 20,10 |
| 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. | 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 |
| 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 | 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 |
