|
6
|
1
|
|
|
2 ;
|
|
|
3 ; User configuration options for Strelka somatic small-variant caller
|
|
|
4 ; workflow:
|
|
|
5 ;
|
|
|
6
|
|
|
7 [user]
|
|
|
8
|
|
|
9 ;
|
|
|
10 ; isSkipDepthFilters should be set to 1 to skip depth filtration for
|
|
|
11 ; whole exome or other targeted sequencing data
|
|
|
12 ;
|
|
|
13 isSkipDepthFilters = 1
|
|
|
14
|
|
|
15 ;
|
|
|
16 ; strelka will not accept input reads above this depth (they will be skipped
|
|
|
17 ; until the depth drops below this value). Set this value <= 0 to disable
|
|
|
18 ; this feature. Using this filter will bound memory usage given extremely high
|
|
|
19 ; depth input, but may be problematic in high-depth targeted sequencing
|
|
|
20 ; applications.
|
|
|
21 ;
|
|
|
22 maxInputDepth = 10000
|
|
|
23
|
|
|
24 ;
|
|
|
25 ; If the depth filter is not skipped, all variants which occur at a
|
|
|
26 ; depth greater than depthFilterMultiple*chromosome mean depth will be
|
|
|
27 ; filtered out.
|
|
|
28 ;
|
|
|
29 depthFilterMultiple = 3.0
|
|
|
30
|
|
|
31 ;
|
|
|
32 ; Somatic SNV calls are filtered at sites where greater than this
|
|
|
33 ; fraction of basecalls have been removed by the mismatch density
|
|
|
34 ; filter in either sample.
|
|
|
35 ;
|
|
|
36 snvMaxFilteredBasecallFrac = 0.4
|
|
|
37
|
|
|
38 ;
|
|
|
39 ; Somatic SNV calls are filtered at sites where greater than this
|
|
|
40 ; fraction of overlapping reads contain deletions which span the SNV
|
|
|
41 ; call site.
|
|
|
42 ;
|
|
|
43 snvMaxSpanningDeletionFrac = 0.75
|
|
|
44
|
|
|
45 ;
|
|
|
46 ; Somatic indel calls are filtered if they represent an expansion or
|
|
|
47 ; contraction of a repeated pattern with a repeat count greater than
|
|
|
48 ; indelMaxRefRepeat in the reference (ie. if indelMaxRefRepeat is 8,
|
|
|
49 ; then the indel is filtered when it is an expansion/contraction of a
|
|
|
50 ; homopolymer longer than 8 bases, a dinucleotide repeat longer than
|
|
|
51 ; 16 bases, etc.)
|
|
|
52 ;
|
|
|
53 indelMaxRefRepeat = 8
|
|
|
54
|
|
|
55 ;
|
|
|
56 ; Somatic indel calls are filtered if greater than this fraction of
|
|
|
57 ; basecalls in a window extending 50 bases to each side of an indel's
|
|
|
58 ; call position have been removed by the mismatch density filter.
|
|
|
59 ;
|
|
|
60 indelMaxWindowFilteredBasecallFrac = 0.3
|
|
|
61
|
|
|
62 ;
|
|
|
63 ; Somatic indels are filtered if they overlap ’interrupted
|
|
|
64 ; homopolymers’ greater than this length. The term 'interrupted
|
|
|
65 ; homopolymer' is used to indicate the longest homopolymer which can
|
|
|
66 ; be found intersecting or adjacent to the called indel when a single
|
|
|
67 ; non-homopolymer base is allowed.
|
|
|
68 ;
|
|
|
69 indelMaxIntHpolLength = 14
|
|
|
70
|
|
|
71 ;
|
|
|
72 ; prior probability of a somatic snv or indel
|
|
|
73 ;
|
|
|
74 ssnvPrior = 0.000001
|
|
|
75 sindelPrior = 0.000001
|
|
|
76
|
|
|
77 ;
|
|
|
78 ; probability of an snv or indel noise allele
|
|
|
79 ;
|
|
|
80 ; NB: in the calling model a noise allele is shared in tumor and
|
|
|
81 ; normal samples, but occurs at any frequency.
|
|
|
82 ;
|
|
|
83 ssnvNoise = 0.0000005
|
|
|
84 sindelNoise = 0.000001
|
|
|
85
|
|
|
86 ;
|
|
|
87 ; Fraction of snv noise attributed to strand-bias.
|
|
|
88 ;
|
|
|
89 ; It is not recommended to change this setting. However, if it is
|
|
|
90 ; essential to turn the strand bias penalization off, the following is
|
|
|
91 ; recommended:
|
|
|
92 ; Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5,
|
|
|
93 ; (1) set ssnvNoiseStrandBiasFrac = 0
|
|
|
94 ; (2) divide the current ssnvNoise value by 2
|
|
|
95 ;
|
|
|
96 ssnvNoiseStrandBiasFrac = 0.5
|
|
|
97
|
|
|
98 ;
|
|
|
99 ; minimum MAPQ score for PE reads at tier1:
|
|
|
100 ;
|
|
|
101 minTier1Mapq = 20
|
|
|
102
|
|
|
103 ;
|
|
|
104 ; minimum MAPQ score for PE and SE reads at tier2:
|
|
|
105 ;
|
|
|
106 minTier2Mapq = 5
|
|
|
107
|
|
|
108 ;
|
|
|
109 ; Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are
|
|
|
110 ; marked as filtered:
|
|
|
111 ;
|
|
|
112 ssnvQuality_LowerBound = 15
|
|
|
113
|
|
|
114 ;
|
|
|
115 ; Somatic quality score (QSI_NT, NT=ref) below which somatic indels
|
|
|
116 ; are marked as filtered:
|
|
|
117 ;
|
|
|
118 sindelQuality_LowerBound = 30
|
|
|
119
|
|
|
120 ;
|
|
|
121 ; Optionally write out read alignments which were altered during the
|
|
|
122 ; realignment step. At the completion of the workflow run, the
|
|
|
123 ; realigned reads can be found in:
|
|
|
124 ;
|
|
|
125 ; ${ANALYSIS_DIR}/realigned/{normal,tumor}.realigned.bam
|
|
|
126 ;
|
|
|
127 isWriteRealignedBam = 0
|
|
|
128
|
|
|
129 ;
|
|
|
130 ; Jobs are parallelized over segments of the reference genome no larger
|
|
|
131 ; than this size:
|
|
|
132 ;
|
|
|
133 binSize = 25000000
|
|
|
134
|
|
|
135 ;
|
|
|
136 ; Additional arguments passed to strelka.
|
|
|
137 ;
|
|
|
138 extraStrelkaArguments =
|
|
|
139
|
