1# CMD line shows the command line used to generate this output
2# DEF lines define expressions for all tested thresholds
3# SN* summary number for every threshold:
4#   1) SN*, filter id
5#   2) number of samples (or trios with -p)
6#   3) number of indel sites total
7#   4) number of indel sites that pass the filter (and, with -p, have a de novo indel)
8#   5) number of indel genotypes that pass the filter (and, with -p, are de novo)
9#   6) number of insertions (site-wise, not genotype-wise)
10#   7) number of deletions (site-wise, not genotype-wise)
11#   8) number of frameshifts (site-wise, not genotype-wise)
12#   9) number of inframe indels (site-wise, not genotype-wise)
13#
14# DVAF* lines report indel variant allele frequency (VAF) distribution for every threshold,
15#   k-th bin corresponds to the frequency k/(nVAF-1):
16#   1) DVAF*, filter id
17#   2) nVAF, number of bins which split the [0,1] VAF interval.
18#   3-22) counts of indel genotypes in the VAF bin. For non-reference hets, the VAF of the less supported allele is recorded
19#
20# DLEN* lines report indel length distribution for every threshold. When genotype fields are available,
21#   the counts correspond to the number of genotypes, otherwise the number of sites are given.
22#   The k-th bin corresponds to the indel size k-MAX_LEN, negative for deletions, positive for insertions.
23#   The first/last bin contains also all deletions/insertions larger than MAX_LEN:
24#   1) DLEN*, filter id
25#   2) maximum indel length
26#   3-43) counts of indel lengths (-max,..,0,..,max), all unique alleles in a genotype are recorded (alt hets increase the counters 2x, alt homs 1x)
27#
28# DFRAC* lines report the mean minor allele fraction at HET indel genotypes as a function of indel size.
29#   The format is the same as for DLEN:
30#   1) DFRAC*, filter id
31#   2) maximum indel length
32#   3-43) mean fraction at indel lengths (-max,..,0,..,max)
33#
34# NFRAC* lines report the number of indels informing the DFRAC distribution.
35#   1) NFRAC*, filter id
36#   2) maximum indel length
37#   3-43) counts at indel lengths (-max,..,0,..,max)
38#
39DEF	FLT0	all
40SN0	6	3	3	5	2	1	1	1
41DVAF0	20	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	1
42DLEN0	20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
43DFRAC0	20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.50	.	.	0.50	0.50	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
44NFRAC0	20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
45