GotCloud: Filters
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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
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 |