--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/conf_file_5.ini	Tue Feb 20 08:31:27 2024 +0000
@@ -0,0 +1,58 @@
+
+#
+# This section contains all configuration settings for the top-level manta workflow,
+#
+[manta]
+
+referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
+
+# Run discovery and candidate reporting for all SVs/indels at or above this size
+# Separate option (to provide different default) used for runs in RNA-mode
+minCandidateVariantSize = 8
+rnaMinCandidateVariantSize = 1000
+
+# Remove all edges from the graph unless they're supported by this many 'observations'.
+# Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted.
+minEdgeObservations = 3
+
+# If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge.
+# Set to 0 to turn this filtration off
+graphNodeMaxEdgeCount = 10
+
+# Run discovery and candidate reporting for all SVs/indels with at least this
+# many spanning support observations
+minCandidateSpanningCount = 3
+
+# After candidate identification, only score and report SVs/indels at or above this size:
+minScoredVariantSize = 50
+
+# minimum VCF "QUAL" score for a variant to be included in the diploid vcf:
+minDiploidVariantScore = 10
+
+# VCF "QUAL" score below which a variant is marked as filtered in the diploid vcf:
+minPassDiploidVariantScore = 20
+
+# minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf:
+minPassDiploidGTScore = 15
+
+# somatic quality scores below this level are not included in the somatic vcf:
+minSomaticScore = 10
+
+# somatic quality scores below this level are filtered in the somatic vcf:
+minPassSomaticScore = 30
+
+# Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote
+# locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads
+# can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime
+# burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read
+# retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling.
+# This feature can be enabled/disabled separately for germline and cancer calling below.
+#
+# Here "CancerCallingModes" includes tumor-normal subtraction and tumor-only calling. "GermlineCallingModes" includes
+# all other calling modes.
+enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1
+enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0
+
+# Set if an overlapping read pair will be considered as evidence
+# Set to 0 to skip overlapping read pairs
+useOverlapPairEvidence = 0