changeset 19:bddc6981a6a7

change version

--- a/strelka.xml	Wed Oct 15 14:43:12 2014 +0200
+++ b/strelka.xml	Wed Oct 15 15:30:28 2014 +0200
@@ -1,4 +1,4 @@
-<tool id="strelka" name="Strelka" version="1.0.0">
+<tool id="strelka" name="Strelka" version="1.0.1">
   <!-- Made by Gregoire Seguin-Henry for geviteam in 2014 -->
   <description>Strelka</description>
   <requirements>

--- a/strelka_config.sample	Wed Oct 15 14:43:12 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,139 +0,0 @@
-
-;
-; 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 = 1
-
-;
-; 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 =
-