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