1# CMD line shows the command line used to generate this output 2# DEF lines define expressions for all tested thresholds 3# FLT* lines report numbers for every threshold and every trio: 4# 1) filter id 5# 2) child 6# 3) father 7# 4) mother 8# 5) number of valid trio genotypes (all trio members pass filters, all non-missing) 9# 6) number of non-reference trio GTs (at least one trio member carries an alternate allele) 10# 7) number of DNMs/Mendelian errors 11# 8) number of novel singleton alleles in the child (counted also as DNM / Mendelian error) 12# 9) number of untransmitted trio singletons (one alternate allele present in one parent) 13# 10) number of transmitted trio singletons (one alternate allele present in one parent and the child) 14# 11) number of transitions, all distinct ALT alleles present in the trio are considered 15# 12) number of transversions, all distinct ALT alleles present in the trio are considered 16# 13) overall ts/tv, all distinct ALT alleles present in the trio are considered 17# 14) number of homozygous DNMs/Mendelian errors (likely genotyping errors) 18# 15) number of recurrent DNMs/Mendelian errors (non-inherited alleles present in other samples; counts GTs, not sites) 19MERR 20 303 child1 father1 mother1 - RECURRENT 20MERR 20 304 child1 father1 mother1 HOM RECURRENT 21MERR 20 305 child1 father1 mother1 HOM - 22TRANSMITTED 20 306 child1 father1 mother1 NO 23TRANSMITTED 20 308 child2 father2 mother2 YES 24TRANSMITTED 20 308 child2 father2 mother2 NO 25MERR 20 309 child1 father1 mother1 - - 26TRANSMITTED 20 310 child1 father1 mother1 NO 27TRANSMITTED 20 311 child2 father2 mother2 YES 28TRANSMITTED 20 312 child1 father1 mother1 YES 29DEF FLT0 all 30FLT0 child1 father1 mother1 14 12 4 2 2 1 3 9 0.33 2 2 31FLT0 child2 father2 mother2 14 11 0 0 1 2 3 9 0.33 0 0 32