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# 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
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