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== Hard Filters ==
== Hard Filters ==
In GotCloud:
{|border="1" cellspacing="0" cellpadding="2"
{|border="1" cellspacing="0" cellpadding="2"
! Filter Prefix !! Filter Description !! Filter if !! Default Value
! Filter Prefix !! Filter Description !! Filter if !! Default Value
| STZ ||Strand Bias z-score || INFO:STZ > FILTER_MAX_STZ < INT_MAX || 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
| 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
| 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
| LQR || || INFO:LQR > FILTER_MAX_LQR/100. < 1 || 30,20
|-
|-
| AOI || Alternate allele inflation score || INFO:AOI > FILTER_MAX_AOI < INT_MAX || 5
| 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
| 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
| 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
| AOZ || Alternate allele quality z-score || INFO:AOZ > FILTER_MAX_AOZ < INT_MAX || off
|-
|}
To remove a filter, set it to blank or "off" in your user configuration file
The values of these filters must be numbers (or comma/space separated list of numbers
These rules apply to the following filters:
* Specifying 1 value in the filter will turn that filter on and use that value.
* Specifying 2 values in the filter (separated by ',' and/or ' ') turns on the filter.
** Use the 1st value if the number of samples is below FILTER_FORMULA_MIN_SAMPLES
** Use the 2nd value if the number of samples is above FILTER_FORMULA_MAX_SAMPLES
** If the number of samples is between the MIN & MAX, a logscale is used:
<pre> (minVal - maxVal) * (log(maxSamples) - log(numSamples)) / (log(maxSamples) - log(minSamples)) + maxVal
</pre>
with:
FILTER_FORMULA_MIN_SAMPLES = 100
FILTER_FORMULA_MAX_SAMPLES = 1000
To add additional filters, set FILTER_ADDITIONAL with the --min/max specified below and the appropriate value, like:
<pre>FILTER_ADDITIONAL = --maxSTP 5 --minLQZ 5</pre>
| FFRQ || || winFFRQ, maxFFRQ both > 0 || 0
{|border="1" cellspacing="0" cellpadding="2"
! Filter Prefix !! Filter Description !! Filter if !! Default Value
|-
| FFRQ || || TBD winFFRQ, maxFFRQ both > 0 ||
|-
|-
| STP || INFO:STP || maxSTP || < INT_MAX ||
| STP || || INFO:STP > maxSTP < INT_MAX ||
|-
|-
| TTT || INFO:TTT || maxTTT || < INT_MAX ||
| TTT || || INFO:TTT > maxTTT < INT_MAX ||
|-
|-
| ttt || INFO:TTT || minTTT || > INT_MIN ||
| ttt || || INFO:TTT < minTTT > INT_MIN ||
|-
|-
| LQZ || INFO:LQZ || maxLQZ || < INT_MAX ||
| LQZ || || INFO:LQZ > maxLQZ < INT_MAX ||
|-
|-
| lqz || INFO:LQZ || minLQZ || > INT_MIN ||
| lqz || || INFO:LQZ < minLQZ > INT_MIN ||
|-
|-
| RBZ || INFO:RBZ || maxRBZ || < INT_MAX ||
| RBZ || || INFO:RBZ > maxRBZ < INT_MAX ||
|-
|-
| rbz || INFO:RBZ || minRBZ || > INT_MIN ||
| rbz || || INFO:RBZ < minRBZ > INT_MIN ||
|-
|-
| CBZ || Cycle Bias z-score || INFO:CBZ > maxCBZ < INT_MAX ||
| CBZ || Cycle Bias z-score || INFO:CBZ > maxCBZ < INT_MAX ||
|-
|-
| cbr || INFO:CBR || minCBR/100. || > -100 ||
| cbr || || INFO:CBR < minCBR/100. > -1 ||
|-
|-
| QBR || INFO:QBR || maxQBR/100. || < 100 ||
| QBR || || INFO:QBR > maxQBR/100. < 1 ||
|-
|-
| qbr || INFO:QBR || minQBR/100. || > -100 ||
| qbr || || INFO:QBR < minQBR/100. > -1 ||
|-
|-
| CSR || INFO:CSR || maxCSR/100. || < 100 ||
| CSR || Cycle-Strand Peason's Correlation || INFO:CSR > maxCSR/100. < 1 ||
|-
|-
| csr || INFO:CSR || minCSR/100. || > -100 ||
| csr || Cycle-Strand Peason's Correlation || INFO:CSR < minCSR/100. > -1 ||
|-
|-
| IOZ || INFO:IOZ || maxIOZ || < INT_MAX ||
| IOZ || Base quality inflation z-score || INFO:IOZ > maxIOZ < INT_MAX ||
|-
|-
| ior || INFO:IOR || minIOR/100. || > INT_MIN ||
| ior || Ratio of base-quality inflation || INFO:IOR < minIOR/100. > INT_MIN/100. ||
|-
|-
| MQ10_ || INFO:MQ10 || maxMQ10/100. || < 100 || off
| MQ10_ || Fraction of bases with mapQ<=10 || INFO:MQ10 > maxMQ10/100. < 1 ||
|-
|-
| MQ20_ || INFO:MQ20 || maxMQ20/100. || < 100 || off
| MQ20_ || Fraction of bases with mapQ<=20 || INFO:MQ20 > maxMQ20/100. < 1 ||
|-
|-
| ABE || INFO:ABE || maxABE/100. || < 100 ||
| ABE || || INFO:ABE > maxABE/100. < 1 ||
|-
|-
| abe || INFO:ABE || minABE/100. || > -100 ||
| abe || || INFO:ABE < minABE/100. > -1 ||
|-
|-
| MBR || INFO:MBR || maxMBR/100. || < 100 ||
| MBR || || INFO:MBR > maxMBR/100. < 1 ||
|-
|-
| mbr || INFO:MBR || minMBR/100. || > -100 ||
| mbr || || INFO:MBR < minMBR/100. > -1 ||
|-
|-
| ABZ || INFO:ABZ || maxABZ || < INT_MAX ||
| ABZ || || INFO:ABZ > maxABZ < INT_MAX ||
|-
|-
| abz || INFO:ABZ || minABZ || > INT_MIN ||
| abz || || INFO:ABZ < minABZ > INT_MIN ||
|-
|-
| BCS || INFO:BCS || maxBCS || < INT_MAX ||
| BCS || || INFO:BCS > maxBCS < INT_MAX ||
|}
|}
