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illumina_pipeline.ini.dummy
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####MAIN CLUSTER CONFIGURATION####
CLUSTER_PATH /opt/sge/default/common
CLUSTER_TMP /tmp
CLUSTER_RESERVATION yes
CLUSTER_PROJECT cog_bioinf
####TOOL PATHS####
# Mapping
BWA_PATH /hpc/local/CentOS7/cog_bioinf/bwa-0.7.5a
SAMBAMBA_PATH /hpc/local/CentOS7/cog_bioinf/sambamba_v0.6.5
# Stats
FASTQC_PATH /hpc/local/CentOS7/cog_bioinf/FastQ-v0.11.4
PICARD_PATH /hpc/local/CentOS7/cog_bioinf/picard-tools-1.141
BAMMETRICS_PATH /hpc/local/CentOS7/cog_bioinf/bamMetrics_v2.1.4
# Gatk
QUEUE_PATH /hpc/local/CentOS7/cog_bioinf/GenomeAnalysisTK-3.8
GATK_PATH /hpc/local/CentOS7/cog_bioinf/GenomeAnalysisTK-3.8
GATK_JAVA_MODULE Java/1.8.0_60
# Annotation
SNPEFF_PATH /hpc/local/CentOS7/cog_bioinf/snpEff_v4.1h
VCFTOOLS_PATH /hpc/local/CentOS7/cog_bioinf/vcftools-0.1.14/bin
# Somatic
STRELKA_PATH /hpc/local/CentOS7/cog_bioinf/strelka_workflow-1.0.14
VARSCAN_PATH /hpc/local/CentOS7/cog_bioinf/varscan-2.4.1/VarScan.v2.4.1.jar
FREEBAYES_PATH /hpc/local/CentOS7/cog_bioinf/freebayes_v1.0.2/bin
MUTECT_PATH /hpc/local/CentOS7/cog_bioinf/mutect-1.1.7
VT_PATH /hpc/local/CentOS7/cog_bioinf/vt_0.5772
# Copy Number
FREEC_PATH /hpc/local/CentOS7/cog_bioinf/freec_v10.4
QDNASEQ_PATH /hpc/local/CentOS7/cog_bioinf/QDNAseq_v1.9.2-HMF.1
# SV
MANTA_PATH /hpc/local/CentOS7/cog_bioinf/manta_1.0.3/bin/
DELLY_PATH /hpc/local/CentOS7/cog_bioinf/delly_v0.7.2
# Other
IGVTOOLS_PATH /hpc/local/CentOS7/cog_bioinf/igvtools-2.3.60
SAMTOOLS_PATH /hpc/local/CentOS7/cog_bioinf/samtools-1.2
TABIX_PATH /hpc/local/CentOS7/cog_bioinf/tabix-0.2.6
PLINK_PATH /hpc/local/CentOS7/cog_bioinf/plink_1.9b3
KING_PATH /hpc/local/CentOS7/cog_bioinf/king_1.4
BIOVCF_PATH /hpc/local/CentOS7/cog/software/bio-vcf-0.9.2/bin
VCFLIB_PATH /hpc/local/CentOS7/cog_bioinf/vcflib_v1.0.0-rc1/bin
BCFTOOLS_PATH /hpc/local/CentOS7/cog_bioinf/bcftools-1.4
HMFTOOLS_PROFILE /hpc/local/CentOS7/cog_bioinf/hmftools_5cdd9f0
####MODES####
PRESTATS yes
MAPPING yes
POSTSTATS yes
INDELREALIGNMENT no
BASEQUALITYRECAL yes
VARIANT_CALLING yes
FILTER_VARIANTS yes
SOMATIC_VARIANTS yes
SV_CALLING yes
COPY_NUMBER yes
BAF yes
FINGERPRINT yes
CALLABLE_LOCI no
ANNOTATE_VARIANTS yes
VCF_UTILS yes
NIPT no
CHECKING yes
QUEUE_RETRY yes
####GENOME SETTINGS####
GENOME /hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.fasta
####SOMATIC SAMPLE REGEX####
SOMATIC_REGEX (CPCT\d{8})([TR][IVX]*$)
SOMATIC_REGEX_REF_CODE R
SOMATIC_REGEX_TUMOR_CODE T
### SOMATIC_REGEX should follow this patern: (<sample_match>)(<origin_match>)
# R = reference
# T = tumor
####PRESTATS CLUSTER CONFIGURATION####
PRESTATS_QUEUE all.q
PRESTATS_TIME 2:0:0
PRESTATS_THREADS 2
PRESTATS_MEM 8
####MAPPING CLUSTER CONFIGURATION####
MAPPING_QUEUE all.q
MAPPING_TIME 8:0:0
MAPPING_THREADS 8
MAPPING_MEM 32
MAPPING_SETTINGS -c 100 -M
MARKDUP_LEVEL sample
MARKDUP_QUEUE all.q
MARKDUP_TIME 8:0:0
MARKDUP_THREADS 8
MARKDUP_MEM 32
MARKDUP_OVERFLOW_LIST_SIZE 500000
####FLAGSTAT CONFIGURATION####
# Used for mapping, realignment and recalibration.
FLAGSTAT_QUEUE all.q
FLAGSTAT_TIME 2:0:0
FLAGSTAT_THREADS 4
FLAGSTAT_MEM 40
####POSTSTATS CLUSTER CONFIGURATION####
POSTSTATS_QUEUE all.q
POSTSTATS_TIME 2:0:0
POSTSTATS_THREADS 2
POSTSTATS_MEM 8
POSTSTATS_COVERAGECAP 250
POSTSTATS_TARGETS /hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/sorted_Homo_sapiens.GRCh37.74_nopseudo_noRNA_CDS_picard.bed
POSTSTATS_BAITS /hpc/cog_bioinf/ENRICH/PICARD/sorted_SS_exome_v5_S04380110_Covered_picard.bed
EXONCALLCOV no
####REALIGNMENT CLUSTER CONFIGURATION####
REALIGNMENT_MASTERQUEUE all.q
REALIGNMENT_MASTERTHREADS 1
REALIGNMENT_MASTERMEM 4
REALIGNMENT_QUEUE all.q
REALIGNMENT_TIME 2:0:0
REALIGNMENT_THREADS 1
REALIGNMENT_MERGETHREADS 1
REALIGNMENT_MEM 4
REALIGNMENT_SCALA QScripts/IndelRealigner.scala
REALIGNMENT_SCATTER 500
REALIGNMENT_MODE single
REALIGNMENT_KNOWN GATK_v2.7/bundle/1000G_phase1.indels.b37.vcf GATK_v2.7/bundle/Mills_and_1000G_gold_standard.indels.b37.vcf
####RECALIBRATION CLUSTER CONFIGURATION####
BASERECALIBRATION_MASTERQUEUE all.q
BASERECALIBRATION_MASTERTHREADS 1
BASERECALIBRATION_MASTERMEM 4
BASERECALIBRATION_QUEUE all.q
BASERECALIBRATION_TIME
BASERECALIBRATION_THREADS 4
BASERECALIBRATION_MEM 16
BASERECALIBRATION_SCALA QScripts/BaseRecalibrator.scala
BASERECALIBRATION_SCATTER 100
BASERECALIBRATION_KNOWN GATK_v2.7/bundle/1000G_phase1.indels.b37.vcf GATK_v2.7/bundle/dbsnp_137.b37.vcf GATK_v2.7/bundle/Mills_and_1000G_gold_standard.indels.b37.vcf
BASERECALIBRATION_QC no
####CALLING CLUSTER CONFIGURATION####
CALLING_MASTERQUEUE all.q
CALLING_MASTERTHREADS 1
CALLING_MASTERMEM 4
CALLING_QUEUE all.q
CALLING_TIME 2:0:0
CALLING_THREADS 1
CALLING_MEM 4
CALLING_SCATTER 1000
CALLING_SCALA QScripts/HaplotypeCaller.scala
CALLING_GVCF no
CALLING_GVCFGQBANDS 5,10,15,20,30,40,50,60 # Must be set when calling_gvcf == yes
CALLING_SEXAWARE no
CALLING_DBSNP bundle/dbsnp_137.b37.vcf
# Optional target interval and padding
CALLING_TARGETS SS_exome_v5_S04380110_Covered_GATK.interval_list
CALLING_INTERVALPADDING 20
CALLING_STANDCALLCONF 10
CALLING_PLOIDY 2
# Only UG
#CALLING_UGMODE BOTH
####VARIANT FILTER CLUSTER CONFIGURATION####
FILTER_MASTERQUEUE all.q
FILTER_MASTERTHREADS 1
FILTER_MASTERMEM 4
FILTER_QUEUE all.q
FILTER_TIME 2:0:0
FILTER_THREADS 1
FILTER_MEM 4
FILTER_SCATTER 10
FILTER_SCALA QScripts/HardFilter.scala
FILTER_MODE BOTH
FILTER_SNPTYPES SNP,NO_VARIATION
FILTER_INDELTYPES INDEL,MIXED
FILTER_SNPNAME SNP_LowQualityDepth SNP_MappingQuality SNP_StrandBias SNP_HaplotypeScoreHigh SNP_MQRankSumLow SNP_ReadPosRankSumLow
FILTER_SNPEXPR QD < 2.0 MQ < 40.0 FS > 60.0 HaplotypeScore > 13.0 MQRankSum < -12.5 ReadPosRankSum < -8.0
FILTER_INDELNAME INDEL_LowQualityDepth INDEL_StrandBias INDEL_ReadPosRankSumLow
FILTER_INDELEXPR QD < 2.0 FS > 200.0 ReadPosRankSum < -20.0
FILTER_CLUSTERSIZE 3
FILTER_CLUSTERWINDOWSIZE 35
####SOMATIC VARIANT CONFIGURATION####
SOMVAR_TARGETS /hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/sorted_Homo_sapiens.GRCh37.74_nopseudo_noRNA_CDS_20bpflanks.bed
SOMVAR_MELT no
SOMVAR_PONFILE /hpc/cog_bioinf/common_dbs/HMF_PON/PON_v2.0.vcf
## Strelka
SOMVAR_STRELKA yes
STRELKA_INI settings/strelka/strelka_config_bwa_genome.ini
STRELKA_QUEUE all.q
STRELKA_TIME 24:0:0
STRELKA_THREADS 6
STRELKA_MEM 60
GIAB_HIGH_CONFIDENCE_BED /hpc/cog_bioinf/common_dbs/GIAB/NIST_v3.3.2/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel.bed
## Varscan
VARSCAN_QUEUE all.q
VARSCAN_TIME 8:0:0
VARSCAN_THREADS 1
VARSCAN_MEM 20
VARSCAN_SETTINGS --min-var-freq 0.1 --strand-filter 1
VARSCAN_POSTSETTINGS --p-value 0.05
PILEUP_QUEUE all.q
PILEUP_TIME 24:0:0
PILEUP_THREADS 12
PILEUP_MEM 60
## Freebayes
SOMVAR_FREEBAYES yes
FREEBAYES_QUEUE all.q
FREEBAYES_TIME 8:0:0
FREEBAYES_THREADS 4
FREEBAYES_TARGETS /hpc/cog_bioinf/ENRICH/PICARD/SS_exome_v5_S04380110_Covered_picard.bed
FREEBAYES_SETTINGS --min-alternate-fraction 0.1 --min-alternate-count 2 --no-partial-observation --pooled-continuous --report-genotype-likelihood-max --allele-balance-priors-off --pooled-discrete --genotype-qualities --min-coverage 5 --no-mnps --no-complex
## Mutect
SOMVAR_MUTECT yes
MUTECT_MEM 5
MUTECT_QUEUE all.q
MUTECT_TIME 8:0:0
MUTECT_THREADS 2
MUTECT_COSMIC /hpc/cog_bioinf/common_dbs/cosmic/CosmicCodingMuts_v72.vcf.gz
## Merge vcfs
SOMVARMERGE_QUEUE all.q
SOMVARMERGE_TIME 2:0:0
SOMVARMERGE_THREADS 6
SOMVARMERGE_MEM 20
####COPY NUMBER VARIANTION CONFIGURATION####
CNVCHECK_QUEUE all.q
CNVCHECK_TIME 2:0:0
CNVCHECK_THREADS 1
CNVCHECK_MEM 4
CNV_MODE sample_control
CNV_TARGETS /hpc/cog_bioinf/data/ies/DESIGNS/sureselect/catalog_designs/SS_all_exon_v5/annotated_S04380110_Covered_genenames.bed
## Contra
CNV_CONTRA yes
CONTRA_THREADS 7
CONTRA_QUEUE all.q
CONTRA_TIME 8:0:0
CONTRA_FLAGS --nomultimapped --largeDeletion --plot
CONTRA_VISUALIZATION yes
CONTRA_PLOTSCRIPT /hpc/cog_bioinf/data/annelies/CNVanalysis/CNA.pl
CONTRA_PLOTDESIGN wes
## QDNASEQ
CNV_QDNASEQ yes
QDNASEQ_QUEUE all.q
QDNASEQ_TIME 8:0:0
QDNASEQ_THREADS 2
QDNASEQ_MEM 40
## FREEC
CNV_FREEC yes
FREEC_THREADS 8
FREEC_QUEUE all.q
FREEC_TIME 8:0:0
FREEC_CHRLENFILE /hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.len
FREEC_CHRFILES /hpc/cog_bioinf/GENOMES/Homo_sapiens.GRCh37.GATK.illumina/chr_files
FREEC_PLOIDY 2
FREEC_WINDOW 1000
FREEC_TELOCENTROMERIC 50000
FREEC_MAPPABILITY_TRACK /hpc/cog_bioinf/common_dbs/hg19_mappability_tracks/out100m2_hg19.gem
#### SV Calling CONFIGURATION####
## DELLY
SV_DELLY no
DELLY_QUEUE all.q
DELLY_TIME 2:0:0
DELLY_MERGE_QUEUE all.q
#DELLY_MERGE_TIME 2:0:0
DELLY_THREADS 4
DELLY_SVTYPE INS DEL DUP INV TRA
DELLY_SPLIT no no no no yes
DELLY_MAPQUAL 1
DELLY_MAD 9
DELLY_FLANK 13
DELLY_VCF_GENO
DELLY_GENO_QUAL 5
## MANTA
SV_MANTA yes
MANTA_QUEUE all.q
MANTA_TIME 4:0:0
MANTA_THREADS 8
MANTA_MEM 10
#### B ALLELE FREQUENCY CLUSTER CONFIGURATION####
BAF_QUEUE all.q
BAF_TIME 2:0:0
BAF_THREADS 2
BAF_MEM 8
BAF_SNPS /hpc/cog_bioinf/common_dbs/CytoScanHD/CytoScanHD_hg19_SNPs_sorted.bed
####FINGERPRINT CONFIGURATION####
FINGERPRINT_QUEUE all.q
FINGERPRINT_THREADS 2
FINGERPRINT_MEM 10
FINGERPRINT_TIME 1:0:0
FINGERPRINT_TARGET /hpc/cog_bioinf/ENRICH/MIPs/81_snps_mip_design_nijmegen_sort.vcf
#### CALLABLE LOCI CLUSTER CONFIGURATION ####
CALLABLE_LOCI yes
CALLABLE_LOCI_QUEUE all.q
CALLABLE_LOCI_TIME 12:0:0
CALLABLE_LOCI_THREADS 1
CALLABLE_LOCI_MEM 10
## HAPLOTYPE CALLER SETTINGS
CALLABLE_LOCI_BASEQUALITY 10
CALLABLE_LOCI_MAPQUALITY 10
CALLABLE_LOCI_DEPTH 20
CALLABLE_LOCI_DEPTHLOWMAPQ 20
####VARIANT ANNOTATION CONFIGURATION####
ANNOTATE_QUEUE all.q
ANNOTATE_TIME 2:0:0
ANNOTATE_THREADS 1
ANNOTATE_MEM 5
## SnpEff
ANNOTATE_SNPEFF yes
ANNOTATE_DB GRCh37.74
ANNOTATE_FLAGS -hgvs -lof -no-downstream -no-upstream -no-intergenic
## SnpSift
ANNOTATE_SNPSIFT yes
ANNOTATE_DBNSFP /hpc/cog_bioinf/common_dbs/dbNSFP/dbNSFPv2.9/dbNSFP2.9.txt.gz
ANNOTATE_FIELDS hg38_chr,hg38_pos,genename,Uniprot_acc,Uniprot_id,Uniprot_aapos,Interpro_domain,cds_strand,refcodon,SLR_test_statistic,codonpos,fold-degenerate,Ancestral_allele,Ensembl_geneid,Ensembl_transcriptid,aapos,aapos_SIFT,aapos_FATHMM,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,LRT_score,LRT_converted_rankscore,LRT_pred,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,MutationAssessor_score,MutationAssessor_rankscore,MutationAssessor_pred,FATHMM_score,FATHMM_rankscore,FATHMM_pred,MetaSVM_score,MetaSVM_rankscore,MetaSVM_pred,MetaLR_score,MetaLR_rankscore,MetaLR_pred,Reliability_index,VEST3_score,VEST3_rankscore,PROVEAN_score,PROVEAN_converted_rankscore,PROVEAN_pred,CADD_raw,CADD_raw_rankscore,CADD_phred,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP46way_primate,phyloP46way_primate_rankscore,phyloP46way_placental,phyloP46way_placental_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phastCons46way_primate,phastCons46way_primate_rankscore,phastCons46way_placental,phastCons46way_placental_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,LRT_Omega,UniSNP_ids,1000Gp1_AC,1000Gp1_AF,1000Gp1_AFR_AC,1000Gp1_AFR_AF,1000Gp1_EUR_AC,1000Gp1_EUR_AF,1000Gp1_AMR_AC,1000Gp1_AMR_AF,1000Gp1_ASN_AC,1000Gp1_ASN_AF,ESP6500_AA_AF,ESP6500_EA_AF,ARIC5606_AA_AC,ARIC5606_AA_AF,ARIC5606_EA_AC,ARIC5606_EA_AF,ExAC_AC,ExAC_AF,ExAC_Adj_AC,ExAC_Adj_AF,ExAC_AFR_AC,ExAC_AFR_AF,ExAC_AMR_AC,ExAC_AMR_AF,ExAC_EAS_AC,ExAC_EAS_AF,ExAC_FIN_AC,ExAC_FIN_AF,ExAC_NFE_AC,ExAC_NFE_AF,ExAC_SAS_AC,ExAC_SAS_AF,clinvar_rs,clinvar_clnsig,clinvar_trait,COSMIC_ID,COSMIC_CNT
## SnpSift annotate eg. GONL
ANNOTATE_FREQUENCIES yes
ANNOTATE_FREQNAME GoNLv5
ANNOTATE_FREQDB /hpc/cog_bioinf/common_dbs/GoNL/gonl_release5/site_freqs/gonl.snps_indels.r5.sorted.vcf.gz
ANNOTATE_FREQINFO AF,AN,AC
## GATK Annotate ID's
ANNOTATE_IDFIELD yes
ANNOTATE_IDNAME Cosmicv72
ANNOTATE_IDDB /hpc/cog_bioinf/common_dbs/cosmic/CosmicCodingMuts_v72.vcf.gz
####VCF UTILS CONFIUGARTION#####
VCFUTILS_QUEUE all.q
VCFUTILS_TIME 2:0:0
VCFUTILS_THREADS 1
VCFUTILS_MEM 8
VCFUTILS_KINSHIP yes
VCFUTILS_GENDERCHECK yes
GENDERCHECK_FEMALE_MAX_F 0.3
GENDERCHECK_MALE_MIN_F 0.7
VCFUTILS_PHASE yes
PED_PATH /path/to/folder/with/ped_files
VCFUTILS_ROH yes
ROH_SETTINGS --AF-dflt 0.4 --ignore-homref --skip-indels
VCFUTILS_SINGLE_SAMPLE_VCF no
####NIPT CLUSTER CONFIGURATION####
NIPT_REFERENCESET /path/to/reference_set/
NIPT_QUEUE all.q
NIPT_MASTERTIME 8:0:0
NIPT_MASTERMEM 30
NIPT_MASTERTHREADS 3
NIPT_TIME 2:0:0
NIPT_MEM off
NIPT_THREADS 4
####CHECKING CLUSTER CONFIGURATION####
CHECKING_QUEUE all.q
CHECKING_TIME 2:0:0
CHECKING_THREADS 1
CHECKING_RM tmp,*.recalibrated.bam,*.recalibrated.bai,*.recalibrated.bam.bai
CHECKING_CLEANUP yes/no
CHECKING_CLEANUP_SCRIPT /path/to/cleanup_script.py