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

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