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annotate configManta.py.ini @ 0:964768ef63f4 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
author artbio
date Tue, 12 May 2020 14:07:23 +0000
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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2 #
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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3 # This section contains all configuration settings for the top-level manta workflow,
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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4 #
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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5 [manta]
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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7 referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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9 # Run discovery and candidate reporting for all SVs/indels at or above this size
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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10 # Separate option (to provide different default) used for runs in RNA-mode
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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11 minCandidateVariantSize = 8
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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12 rnaMinCandidateVariantSize = 1000
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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14 # Remove all edges from the graph unless they're supported by this many 'observations'.
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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15 # Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted.
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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16 minEdgeObservations = 3
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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18 # If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge.
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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19 # Set to 0 to turn this filtration off
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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20 graphNodeMaxEdgeCount = 10
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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22 # Run discovery and candidate reporting for all SVs/indels with at least this
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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23 # many spanning support observations
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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24 minCandidateSpanningCount = 3
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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26 # After candidate identification, only score and report SVs/indels at or above this size:
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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27 minScoredVariantSize = 50
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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29 # minimum VCF "QUAL" score for a variant to be included in the diploid vcf:
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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30 minDiploidVariantScore = 10
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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32 # VCF "QUAL" score below which a variant is marked as filtered in the diploid vcf:
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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33 minPassDiploidVariantScore = 20
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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35 # minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf:
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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36 minPassDiploidGTScore = 15
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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38 # somatic quality scores below this level are not included in the somatic vcf:
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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39 minSomaticScore = 10
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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41 # somatic quality scores below this level are filtered in the somatic vcf:
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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42 minPassSomaticScore = 30
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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44 # Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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45 # locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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46 # can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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47 # burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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48 # retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling.
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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49 # This feature can be enabled/disabled separately for germline and cancer calling below.
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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50 #
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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51 # Here "CancerCallingModes" includes tumor-normal subtraction and tumor-only calling. "GermlineCallingModes" includes
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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52 # all other calling modes.
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53 enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1
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54 enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0
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56 # Set if an overlapping read pair will be considered as evidence
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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57 # Set to 0 to skip overlapping read pairs
964768ef63f4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 64ca39116562f6749822a2933df8ae5afc520b3e"
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58 useOverlapPairEvidence = 0