run_sm_counter_v2.params.txt

[general]
# tools
cutadaptDir = /opt/conda/bin/
bwaDir      = /opt/conda/bin/
samtoolsDir = /srv/qgen/bin/samtools-1.5/bin/
javaExe     = /opt/conda/jre/bin/java

# ssw for fast Smith-Waterman
sswPyFile = /srv/qgen/bin/ssw/src/ssw_wrap.py

# Ion torrent tools
torrentBinDir = /srv/qgen/bin/TorrentSuite/
vcflibDir = /srv/qgen/bin/vcflib/bin/

# quandico
quandicoDir = /srv/qgen/code/qiaseq-dna/quandico/

# general params
numCores = 0
deleteLocalFiles = False
samtoolsMem = 2500M
outputDetail = True

# prep module - read preparation (common region trimming) params
trimScript = /srv/qgen/code/qiaseq-dna/core/prep_trim.py

# geneome file
genomeFile = /srv/qgen/data/genome/ucsc.hg19.fa

# umi module
endogenousLenMin = 15

# SAM tag names
tagNameUmiSeq   = mi
tagNameUmi      = Mi
tagNamePrimer   = pr
tagNameResample = re

# variant primitive to complex conversion
vcfComplexGapMax = 3

# variant annotation
snpEffPath   = /opt/conda/share/snpeff-4.2-0/
snpEffConfig = /opt/conda/share/snpeff-4.2-0/snpEff.config
dbSnpFile    = /srv/qgen/data/annotation/common_all_20160601.vcf.gz
cosmicFile   = /srv/qgen/data/annotation/CosmicAllMuts_v69_20140602.vcf.gz
clinVarFile  = /srv/qgen/data/annotation/clinvar_20160531.vcf.gz

# variant caller parameters (these need a separate section)
[smCounter]
minBQ = 25 
minMQ = 50 
hpLen = 8 
mismatchThr = 6.0 
mtThreshold = 0.8
minAltUMI = 3
maxAltAllele = 2
primerDist = 2 
repBed = /srv/qgen/data/annotation/simpleRepeat.full.bed
srBed = /srv/qgen/data/annotation/SR_LC_SL.full.bed

# readSet
[NEB_S2]
readFile1 = /srv/qgen/example/NEB_S2_L001_R1_001.fastq.gz
readFile2 = /srv/qgen/example/NEB_S2_L001_R2_001.fastq.gz
primerFile = /srv/qgen/example/DHS-101Z.primers.txt
roiBedFile = /srv/qgen/example/DHS-101Z.roi.bed
platform = Illumina
runCNV = False
sampleType =  Single
duplex = False