annotate test-data/conf_file_3.ini @ 7:555971edd46e draft default tip

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