--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/strelka_config_bwa_default.ini	Wed Oct 15 14:43:12 2014 +0200
@@ -0,0 +1,139 @@
+
+;
+; User configuration options for Strelka somatic small-variant caller
+; workflow:
+;
+
+[user]
+
+;
+; isSkipDepthFilters should be set to 1 to skip depth filtration for
+; whole exome or other targeted sequencing data
+;
+isSkipDepthFilters = 0
+
+;
+; strelka will not accept input reads above this depth (they will be skipped
+; until the depth drops below this value). Set this value <= 0 to disable
+; this feature. Using this filter will bound memory usage given extremely high
+; depth input, but may be problematic in high-depth targeted sequencing
+; applications.
+;
+maxInputDepth = 10000
+
+;
+; If the depth filter is not skipped, all variants which occur at a
+; depth greater than depthFilterMultiple*chromosome mean depth will be
+; filtered out.
+;
+depthFilterMultiple = 3.0
+
+;
+; Somatic SNV calls are filtered at sites where greater than this
+; fraction of basecalls have been removed by the mismatch density
+; filter in either sample.
+;
+snvMaxFilteredBasecallFrac = 0.4
+
+;
+; Somatic SNV calls are filtered at sites where greater than this
+; fraction of overlapping reads contain deletions which span the SNV
+; call site.
+;
+snvMaxSpanningDeletionFrac = 0.75
+
+;
+; Somatic indel calls are filtered if they represent an expansion or
+; contraction of a repeated pattern with a repeat count greater than
+; indelMaxRefRepeat in the reference (ie. if indelMaxRefRepeat is 8,
+; then the indel is filtered when it is an expansion/contraction of a
+; homopolymer longer than 8 bases, a dinucleotide repeat longer than
+; 16 bases, etc.)
+;
+indelMaxRefRepeat = 8
+
+;
+; Somatic indel calls are filtered if greater than this fraction of
+; basecalls in a window extending 50 bases to each side of an indel's
+; call position have been removed by the mismatch density filter.
+;
+indelMaxWindowFilteredBasecallFrac = 0.3
+
+;
+; Somatic indels are filtered if they overlap ’interrupted
+; homopolymers’ greater than this length. The term 'interrupted
+; homopolymer' is used to indicate the longest homopolymer which can
+; be found intersecting or adjacent to the called indel when a single
+; non-homopolymer base is allowed.
+;
+indelMaxIntHpolLength = 14
+
+;
+; prior probability of a somatic snv or indel
+;
+ssnvPrior = 0.000001
+sindelPrior = 0.000001
+
+;
+; probability of an snv or indel noise allele 
+;
+; NB: in the calling model a noise allele is shared in tumor and
+; normal samples, but occurs at any frequency.
+;
+ssnvNoise = 0.0000005
+sindelNoise = 0.000001
+
+;
+; Fraction of snv noise attributed to strand-bias.
+;
+; It is not recommended to change this setting. However, if it is
+; essential to turn the strand bias penalization off, the following is
+; recommended:
+; Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5,
+; (1) set ssnvNoiseStrandBiasFrac = 0
+; (2) divide the current ssnvNoise value by 2
+;
+ssnvNoiseStrandBiasFrac = 0.5
+
+;
+; minimum MAPQ score for PE reads at tier1:
+;
+minTier1Mapq = 20
+
+;
+; minimum MAPQ score for PE and SE reads at tier2:
+;
+minTier2Mapq = 5
+
+;
+; Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are
+; marked as filtered:
+;
+ssnvQuality_LowerBound = 15
+
+;
+; Somatic quality score (QSI_NT, NT=ref) below which somatic indels
+; are marked as filtered:
+;
+sindelQuality_LowerBound = 30
+
+;
+; Optionally write out read alignments which were altered during the
+; realignment step. At the completion of the workflow run, the
+; realigned reads can be found in:
+;
+; ${ANALYSIS_DIR}/realigned/{normal,tumor}.realigned.bam
+;
+isWriteRealignedBam = 0
+
+;
+; Jobs are parallelized over segments of the reference genome no larger
+; than this size:
+;
+binSize = 25000000
+
+;
+; Additional arguments passed to strelka.
+;
+extraStrelkaArguments =
+