# 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)
MERR	20	303	child1	father1	mother1	-	RECURRENT
MERR	20	304	child1	father1	mother1	HOM	RECURRENT
MERR	20	305	child1	father1	mother1	HOM	-
TRANSMITTED	20	306	child1	father1	mother1	NO
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
DEF	FLT0	all
FLT0	child1	father1	mother1	14	12	4	2	2	1	3	9	0.33	2	2
FLT0	child2	father2	mother2	14	11	0	0	1	2	3	9	0.33	0	0
