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annotate test-data/conf_file_2.ini @ 7:555971edd46e draft default tip

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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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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
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diff changeset
1 [manta]
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
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diff changeset
2 referenceFasta = /dummy/path/to/genome.fa
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
diff changeset
3 enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
diff changeset
4 minPassSomaticScore = 30
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
diff changeset
5 minSomaticScore = 10
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
diff changeset
6 minCandidateVariantSize = 8
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
diff changeset
7 minPassDiploidVariantScore = 20
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
diff changeset
8 useOverlapPairEvidence = 0
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
diff changeset
9 minPassDiploidGTScore = 15
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
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diff changeset
10 graphNodeMaxEdgeCount = 10
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
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diff changeset
11 minEdgeObservations = 3
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
diff changeset
12 minDiploidVariantScore = 10
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
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diff changeset
13 minCandidateSpanningCount = 3
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
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14 enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
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diff changeset
15 rnaMinCandidateVariantSize = 1000
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
artbio
parents:
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16 minScoredVariantSize = 50