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comparison lib/strelka_config_eland_default.ini @ 18:3c10d88b55ad

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improved user interface
author mini
date Wed, 15 Oct 2014 14:43:12 +0200
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17:8260a4188b08 18:3c10d88b55ad
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 = 0
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 = 0.0000001
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 = 40
102
103 ;
104 ; minimum MAPQ score for PE and SE reads at tier2:
105 ;
106 minTier2Mapq = 5
107
108
109 ;
110 ; Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are
111 ; marked as filtered:
112 ;
113 ssnvQuality_LowerBound = 15
114
115 ;
116 ; Somatic quality score (QSI_NT, NT=ref) below which somatic indels
117 ; are marked as filtered:
118 ;
119 sindelQuality_LowerBound = 30
120
121 ;
122 ; Optionally write out read alignments which were altered during the
123 ; realignment step. At the completion of the workflow run, the
124 ; realigned reads can be found in:
125 ;
126 ; ${ANALYSIS_DIR}/realigned/{normal,tumor}.realigned.bam
127 ;
128 isWriteRealignedBam = 0
129
130 ;
131 ; Jobs are parallelized over segments of the reference genome no larger
132 ; than this size:
133 ;
134 binSize = 25000000
135
136 ;
137 ; Additional arguments passed to strelka.
138 ;
139 extraStrelkaArguments = --eland-compatibility
140