#
# 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:
minCandidateVariantSize = 8

# 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

# 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 = 51

# 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