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config.yaml
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config.yaml
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### Reference
# General settings
reference:
release: 111
nonchr: false
threads: 30
mapq: 30 # overall required mapping quality
basequal: 20 # overall required base quality
data:
name: samplename
dnaseq:
dna_tumor: <path/to/reads>
rnaseq:
rna_tumor: <path/to/to/reads>
normal: <normal/sample/identifier>
custom:
variants:
hlatyping:
MHC-I:
MHC-II:
### pre-processing (only applied on fastq reads)
preproc:
activate: true # whether (=true) or not (=false) to include pre-processing
minlen: 10
slidingwindow:
activate: true
wsize: 3
wqual: 20
### alingment
align:
chimSegmentMin: 20
chimScoreMin: 10
chimJunctionOverhangMin: 10
chimScoreDropMax: 30
chimScoreSeparation: 10
### variant calling
# alternative splicing
altsplicing:
activate: true # whether (=true) or not (=false) to include alternative splicing events
confidence: 3 # confidence level (1,2 or 3) - filtering of input alignments
iterations: 5 # number of iteratios (when adding intro edges) - increases sensitivity
edgelimit: 250 # limit max number of edges in graph - affects the runtime
# exitron splicing
exitronsplicing:
activate: true # whether (=true) or not (=false) to include exitron-splicing events
ao: 3 # allele observation
pso: 0.05 # percent spliced out
strand: 1 # strand specificity of library (0=unstranded, 1=forward, 2=reverse)
# gene fusion
genefusion:
activate: true # whether (=true) or not (=false) to include gene fusion events
maxevalue: 0.3
suppreads: 2 # all fusions with less than suppreads are discarded
maxsuppreads: 1000
maxidentity: 0.3 # genes with fraction of identity are discarded (homologs)
hpolymerlen: 6 # removes breakpoints adjacent to homopolymers of length
readthroughdist: 10000 # distance between breakpoints with less than distance
minanchorlen: 20 # removes fusions whose segments are less than minchimlen
splicedevents: 4 # fusions between genes need at least this many spliced breakpoints
maxkmer: 0.6 # remove reads with repetitive 3-mer that make up more than maxkmer
fraglen: 200 # mean fragment length
maxmismatch: 0.01
### indel
indel:
activate: true # whether (=true) or not (=false) to include indels
type: all # long, short, all
mode: BOTH # DNA, RNA or BOTH -
# strategy for optimizing posterior probability threshold
strategy: OPTIMAL_F_SCORE # OPTIMAL_F_SCORE, FALSE_DISCOVERY_RATE, CONSTANT
fscorebeta: 1.0 # rel. weight of recall to precision (when OPTIMAL_F_SCORE is selected)
fdr: 0.05 # false discovery rate (when FALSE_DISCOVERY_RATE is selected)
sliplen: 8 # min number of reference bases to suspect slippage event
sliprate: 0.1 # frequency of slippage when it is supsected
quantification:
mode: BOTH # RNA, RNA or BOTH
hlatyping:
class: BOTH # I, II or BOTH
# specific path for class II hlatyping (only required when class: II, or BOTH)
MHC-I_mode: DNA, RNA # DNA, RNA, or custom (if empty alleles have to be specified in custom)
MHC-II_mode: DNA, RNA # DNA, RNA, or custom (if empty alleles have to be specified in custom)
# specific path for class II hlatyping (only required when class: II, or BOTH)
freqdata: ./hlahd_files/freq_data/
split: ./hlahd_files/HLA_gene.split.txt
dict: ./hlahd_files/dictionary/
prioritization:
class: I # I, II or BOTH
lengths:
MHC-I: 8,9,10,11
MHC-II: 13,14,15