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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
author artbio
date Tue, 20 Feb 2024 08:31:27 +0000
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6:cb5691381acb 7:555971edd46e
1
2 #
3 # This section contains all configuration settings for the top-level manta workflow,
4 #
5 [manta]
6
7 referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
8
9 # Run discovery and candidate reporting for all SVs/indels at or above this size
10 # Separate option (to provide different default) used for runs in RNA-mode
11 minCandidateVariantSize = 8
12 rnaMinCandidateVariantSize = 1000
13
14 # Remove all edges from the graph unless they're supported by this many 'observations'.
15 # Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted.
16 minEdgeObservations = 3
17
18 # If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge.
19 # Set to 0 to turn this filtration off
20 graphNodeMaxEdgeCount = 10
21
22 # Run discovery and candidate reporting for all SVs/indels with at least this
23 # many spanning support observations
24 minCandidateSpanningCount = 3
25
26 # After candidate identification, only score and report SVs/indels at or above this size:
27 minScoredVariantSize = 50
28
29 # minimum VCF "QUAL" score for a variant to be included in the diploid vcf:
30 minDiploidVariantScore = 10
31
32 # VCF "QUAL" score below which a variant is marked as filtered in the diploid vcf:
33 minPassDiploidVariantScore = 20
34
35 # minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf:
36 minPassDiploidGTScore = 15
37
38 # somatic quality scores below this level are not included in the somatic vcf:
39 minSomaticScore = 10
40
41 # somatic quality scores below this level are filtered in the somatic vcf:
42 minPassSomaticScore = 30
43
44 # Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote
45 # locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads
46 # can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime
47 # burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read
48 # retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling.
49 # This feature can be enabled/disabled separately for germline and cancer calling below.
50 #
51 # Here "CancerCallingModes" includes tumor-normal subtraction and tumor-only calling. "GermlineCallingModes" includes
52 # all other calling modes.
53 enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1
54 enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0
55
56 # Set if an overlapping read pair will be considered as evidence
57 # Set to 0 to skip overlapping read pairs
58 useOverlapPairEvidence = 0