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