# VariTAS pipeline config file
#

package_name: varitas

### ANNOTATION SETTINGS

annotation_method: GENCODE
reference_build: grch37


### VARIANT FILTERS

# SUPPORTED FILTERS:
#   min_tumour_depth, min_normal_depth
#   min_tumour_variant_reads, max_normal_variant_reads
#   min_tumour_allele_frequency, max_normal_allele_frequency
#   ct_min_tumour_allele_frequency: a separate minimum tumour allele frequency applied to C>T substitutions (attempt to filter out FFPE artefacts)
#   indel_min_tumour_allele_frequency: minimum allele frequency for indels
#   remove_1000_genomes: remove anything that appears in the 1000 genomes project (useful when no normal filter available, e.g. for PGM output or unpaired calling)
#   remove_germline_status: remove variants with STATUS field set to germline
#
# In the case of variant calling without normals, all filters with 'normal' in the
# name will be ignored
filters:
  mutect:
    min_tumour_variant_reads: 5
    min_tumour_allele_frequency: 0.05
    ct_min_tumour_allele_frequency: 0.01
  pgm:
    min_tumour_variant_reads: 5
    min_tumour_allele_frequency: 0.01
    remove_1000_genomes: true
    ct_min_tumour_allele_frequency: 0.01
    indel_min_tumour_allele_frequency: 0.02
  vardict:
    min_tumour_variant_reads: 5
    min_tumour_allele_frequency: 0.01
    ct_min_tumour_allele_frequency: 0.01
    indel_min_tumour_allele_frequency: 0.02
    remove_germline_status: true
  varscan:
    min_tumour_variant_reads: 5
    min_tumour_allele_frequency: 0.01
    remove_germline_status: true
  lofreq:
    min_tumour_variant_reads: 5
    min_tumour_allele_frequency: 0.01
    remove_germline_status: true
  consensus:
    min_tumour_allele_frequency: 0.01
    ct_min_tumour_allele_frequency: 0.01

# Fields in final variant call output file
# ANNOTATION_DB will be replaced by the annotation database in question (determined by annotation_method and reference_build)
annovar_fields:
  - CHROM
  - POS
  - REF
  - ALT
  - Func.ANNOTATION_DB
  - ExonicFunc.ANNOTATION_DB
  - Gene.ANNOTATION_DB
  - AAChange.ANNOTATION_DB
  - cosmic70
  - 1000g2015aug_all
  - cytoBand
  - ExAC_nontcga_ALL
  - CLNDBN
  - STATUS
  - QUAL
  - SIFT_score
  - Polyphen2_HDIV_score
  - Interpro_domain

annovar_genotype_fields:
  - DP
  - GT
  - AF
  - AD


### SEQUENCING SETTINGS
# should be either illumina or ION_TORRENT
sequencing_platform: ION_TORRENT
target_panel:

# path to reference FASTA, Must have corresponding sequence dictionary
reference_genome:
  grch37: /path/to/dna/hg19.fa
  grch38: /path/to/dna/GRCh38.d1.vd1.fa
barcode: CTTGTA

### CLUSTER SETTINGS

# Note: this num_cpu is probably just for a single job... rename or phase out
num_cpu: 5
project_code: abcd
cluster_scheduler: LSF


### APPLICATION SETTINGS

# iDES
ides_path: /path/to/iDES/v1.1/

# Annovar (need to update database)
annovar_path: /apps/annovar/20160201/
annovar_database:
  grch37: /path/to/GRCh37/annovar/20170601/
  grch38: /path/to/annovar/20170601/

# Version numbers for module loading
#  – these must match available modules
bwa_version: 0.7.12
bedtools_version: 2.25.0
java_version: sun8/1.8.0u66
samtools_version: 1.5
picardtools_version: 2.1.0
vardictjava_version: 1.4.6
fastqc_version: 0.11.4
r_version: 3.5.0

# Picard
# want this to match version above
picard_jar: /apps/picard-tools/2.1.0/picard.jar

# GATK
gatk_jar: /apps/gatk/4.0.5.1/gatk-package-4.0.5.1-local.jar

# MuTect
dbsnp_vcf: /path/to/dbsnp/00-common_all.chr.vcf
cosmic_vcf: /path/to/cosmic/CosmicCodingMuts.chr.vcf
#-
mutect_gatk_jar: /apps/gatk/4.0.5.1/gatk-package-4.0.5.1-local.jar

# MuSE
muse_path: /path/to/MuSE/MuSE

# VarScan
varscan_path: /path/to/VarScan.v2.4.3.jar

# LoFreq
lofreq_path: /path/to/lofreq_star-2.1.3.1/bin/lofreq

# VarDict
vardict_path: /path/to/VarDict/20170831/
