# CMD line shows the command line used to generate this output
# DEF lines define expressions for all tested thresholds
# FLT* lines report numbers for every threshold and every trio:
#   1) filter id
#   2) child
#   3) father
#   4) mother
#   5) number of valid trio genotypes (all trio members pass filters, all non-missing)
#   6) number of non-reference trio GTs (at least one trio member carries an alternate allele)
#   7) number of DNMs/Mendelian errors
#   8) number of novel singleton alleles in the child (counted also as DNM / Mendelian error)
#   9) number of untransmitted trio singletons (one alternate allele present in one parent)
#   10) number of transmitted trio singletons (one alternate allele present in one parent and the child)
#   11) number of transitions, all distinct ALT alleles present in the trio are considered
#   12) number of transversions, all distinct ALT alleles present in the trio are considered
#   13) overall ts/tv, all distinct ALT alleles present in the trio are considered
#   14) number of homozygous DNMs/Mendelian errors (likely genotyping errors)
#   15) number of recurrent DNMs/Mendelian errors (non-inherited alleles present in other samples; counts GTs, not sites)
TRANSMITTED	20	302	child2	father2	mother2	YES
MERR	20	303	child1	father1	mother1	-	RECURRENT
TRANSMITTED	20	303	child2	father2	mother2	YES
MERR	20	304	child1	father1	mother1	HOM	RECURRENT
TRANSMITTED	20	304	child2	father2	mother2	YES
MERR	20	305	child1	father1	mother1	HOM	-
TRANSMITTED	20	306	child1	father1	mother1	NO
TRANSMITTED	20	307	child2	father2	mother2	YES
TRANSMITTED	20	308	child2	father2	mother2	YES
TRANSMITTED	20	308	child2	father2	mother2	NO
MERR	20	309	child1	father1	mother1	-	-
TRANSMITTED	20	310	child1	father1	mother1	NO
TRANSMITTED	20	311	child2	father2	mother2	YES
TRANSMITTED	20	312	child1	father1	mother1	YES
TRANSMITTED	20	315	child1	father1	mother1	YES
TRANSMITTED	20	315	child2	father2	mother2	NO
DEF	FLT0	all
FLT0	child1	father1	mother1	14	12	4	2	2	2	3	9	0.33	2	2
FLT0	child2	father2	mother2	14	11	0	0	2	6	3	9	0.33	0	0
