GotCloud: Filters

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		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/100. < INT_MAX/100.	off
AOZ	Alternate allele quality z-score	INFO:AOZ > FILTER_MAX_AOZ < INT_MAX	off
FFRQ		winFFRQ, maxFFRQ both > 0	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.	> -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
MQ10_	INFO:MQ10	maxMQ10/100.	< 100	off
MQ20_	INFO:MQ20	maxMQ20/100.	< 100	off
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