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

See Hard Filtering Options for configuration settings having to do with hard filters.

In GotCloud:

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 < 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:

      (minVal - maxVal) * (log(maxSamples) - log(numSamples)) / (log(maxSamples) - log(minSamples)) + maxVal

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:

FILTER_ADDITIONAL = --maxSTP 5 --minLQZ 5

Filter Prefix	Filter Description	Filter if
FFRQ		TBD winFFRQ, maxFFRQ both > 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. > -1
QBR		INFO:QBR > maxQBR/100. < 1
qbr		INFO:QBR < minQBR/100. > -1
CSR	Cycle-Strand Peason's Correlation	INFO:CSR > maxCSR/100. < 1
csr	Cycle-Strand Peason's Correlation	INFO:CSR < minCSR/100. > -1
IOZ	Base quality inflation z-score	INFO:IOZ > maxIOZ < INT_MAX
ior	Ratio of base-quality inflation	INFO:IOR < minIOR/100. > INT_MIN/100.
MQ10_	Fraction of bases with mapQ<=10	INFO:MQ10 > maxMQ10/100. < 1
MQ20_	Fraction of bases with mapQ<=20	INFO:MQ20 > maxMQ20/100. < 1
ABE		INFO:ABE > maxABE/100. < 1
abe		INFO:ABE < minABE/100. > -1
MBR		INFO:MBR > maxMBR/100. < 1
mbr		INFO:MBR < minMBR/100. > -1
ABZ		INFO:ABZ > maxABZ < INT_MAX
abz		INFO:ABZ < minABZ > INT_MIN
BCS		INFO:BCS > maxBCS < INT_MAX