Input Parameters

Multiple parameters can be set with ACEseq though not all are necessary to change. This table gives and overview and description for all available parameters

“ACEseq parameters”
name value type description
aceseqOutputDirectory ${outputAnalysisBaseDirectory}/ACEseq_${tumorSample} path  
svOutputDirectory ${outputAnalysisBaseDirectory}/SV_calls path  
crestOutputDirectory ${outputAnalysisBaseDirectory}/crest path  
cnvSnpOutputDirectory ${aceseqOutputDirectory}/cnv_snp path  
imputeOutputDirectory ${aceseqOutputDirectory}/phasing path  
plotOutputDirectory ${aceseqOutputDirectory}/plots path  
runWithoutControl false boolean use control for analysis (false|true)
minHT 5 integer minimum number of consecutive SNPs to be considered for haploblocks
snp_min_coverage 5 integer minimum coverage in control for SNP
cnv_min_coverage 5000 integer minimum coverage for 1kb windows to be considered for merging in 10kb windows
mapping_quality 1000 integer minimum mapping quality for 1kb windows to be considered for merging in 10kb windows (maximum mappability)
min_windows 5 integer minimum number of 1kb windows fullfilling cnv_min_coverage and mapping_quality to obtain merged 10kb windows
min_X_ratio 0.8 float minimum ratio for number of reads on chrY per base over number of reads per base over whole genome to be considered as female
min_Y_ratio 0.12 float minimum ratio for number of reads on chrY per base over number of reads per base over whole genome to be considered as male
LOWESS_F 0.1 float f parameter for R lowess function
SCALE_FACTOR 0.9 float scale_factor for R lowess function
COVERAGEPLOT_YLIMS 4 float ylims for Rplots in GC-bias plots
FILENAME_GC_CORRECT_PLOT ${plotOutputDirectory}/${pid}_gc_corrected.png path gc-bias plot, before/during/after correction
GC_bias_json_key gc-bias string key in GC-bias json
FILE_DENSITYBETA ${aceseqOutputDirectory}/densityBeta.pdf path  
min_DDI_length 1000 integer minimum length for DEL/DUP/INV to be considered for breakpoint integration
selSVColumn eventScore string column from bedpe file to be recored in ${pid}_sv_points.txt file
min_seg_width 2000 integer segmentByPairedPSCBS() minwidth parameter in PSCBS R package
undo_SD 24 integer segmentByPairedPSCBS() undo.SD parameter in PSCBS R package
pscbs_prune_height 0 integer pruneByHClust() parameter h in PSCBS R package
min_segment_map 0.6 float minimum average mappability over segment to be kept after segmentation
min_seg_length_prune 9000 integer maximum of segment to be considered for merging to neighbouring segment prior to clustering
min_num_SNPs 15 integer maximum number of SNPs in segment to be considered for merging to neighbouring segment prior to clustering
clustering yes string should segments be clustered (yes|no), coerage and BAF will be estimated and assigned clusterwide
min_cluster_number 1 integer minimum number of clusters to be tried with BIC
min_membership 0.8 float obsolete
min_distance 0.05 float min_distance
haplogroupFilePrefix haploblocks_chr string prefix for file with haplogroups per chromosome
haplogroupFileSuffix txt string suffix for file with haplogroups per chromosome
haplogroupFilePath ${imputeOutputDirectory}/${haplogroupFilePrefix} path  
min_length_purity 1000000 integer minimum length of segments to be considered for tumor cell content and ploidy estimation
min_hetSNPs_purity 500 integer minimum number of control heterozygous SNPs in segments to be considered for tumor cell content and ploidy estimation
dh_stop max string  
min_length_dh_stop 1000000 integer  
dh_zero no string  
purity_min 0.3 float minimum tumor cell content allowed
purity_max 1.0 float i
ploidy_min 1.0 float  
ploidy_max 6.5 float  
SNP_VCF_CNV_PATH ${cnvSnpOutputDirectory}/${pid}.chr path If the value is changed the value for the filename pattern MUST also be changed.
SNP_VCF_CNV_PATH_STR ${SNP_VCF_CNV_PATH} string This value must be converted to a string because of a bug.
SNP_SUFFIX snp.tab.gz string  
       
CHR_NR ${CHR_PREFIX}${PARM_CHR_INDEX}${CHR_SUFFIX} string  
CHR_NAME ${PARM_CHR_INDEX} string  
AUTOSOME_INDICES ( {1..22} ) bashArray  
CREST yes string include SV breakpoints in analysis (yes|no)
mpileup_qual 0 integer quality used for parameter ‘Q’ in samtools mpileup
CNV_MPILEUP_OPTS “-A -R -B -Q ${mpileup_qual} -q 1 -I “ string options for mpileup to determine which bases/reads to use
FILE_VCF_SUF vcf string suffix for vcf files
FILE_TXT_SUF txt string suffix for txt files
phasedGenotypesFilePrefix phased_chr string prefix for phased genotypes file
unphasedGenotypesFilePrefix unphased_chr string prefix for unphased genotypes file
phasedGenotypesFileSuffix ${FILE_VCF_SUF} string suffix for phased genotypes file
unphasedGenotypesFileSuffix ${FILE_VCF_SUF} string suffix for unphased genotypes file
BCFTOOLS_OPTS “-vgN “ string bcftools options for imputation
FAKE_CONTROL_POST .cnv.anno.tab.gz string suffix for chromosome wise 1kb coverage files used for fake control workflow
PATIENTSEX male string patient sex used in case of no control workflow (male|female|klinefelter)
CNV_ANNO_SUFFIX cnv.anno.tab.gz string suffix for mappability annotated chromosome-wise 1kb coverage files
CNV_SUFFIX cnv.tab.gz string suffix chromosome-wise 1kb coverage files
FILE_UNPHASED_PRE ${imputeOutputDirectory}/${unphasedGenotypesFilePrefix} path  
FILE_UNPHASED_GENOTYPE ${imputeOutputDirectory}/unphased_genotype_chr path  
FILE_PHASED_PRE ${imputeOutputDirectory}/${phasedGenotypesFilePrefix} path  
FILE_PHASED_GENOTYPE ${imputeOutputDirectory}/phased_genotype_chr path  
FILE_INFO info string  
FILE_INFO_SAMPLE info_by_sample string  
FILE_HAPS haps string  
FILE_HAPS_CONF haps_confidence string  
FILE_SUMMARY summary string  
FILE_WARNINGS warnings string  
FILE_PART part string  
FILE_SAMPLE_G ${imputeOutputDirectory}/sample_g.txt path sample_g file used by imputation on X chromosome for females
MALE_FAKE_CONTROL_PRE ${pathToACEseqResults}/cnv_snp/${pid}.chr path path and prefix to chromosome-wise 1kb coverage file used for fake control workflow for male patients
FEMALE_FAKE_CONTROL_PRE ${pathToACEseqResults}/cnv_snp/${pid}.chr path path and prefix to chromosome-wise 1kb coverage file used for fake control workflow for female patients
PLOT_PRE ${aceseqOutputDirectory}/${pid}_plot path  
FILE_MOST_IMPORTANT_INFO_SEG_PRE ${pid}_most_important_info string  
FILE_MOST_IMPORTANT_INFO_SEG_POST .txt string  
FILE_SEGMENT_VCF_PRE ${aceseqOutputDirectory}/${pid} path  
FILE_SEGMENT_VCF_POST .cnv.vcf string  
outputUMask 007 string  
outputFileGroup $accessGroup   group for output files and directories
outputAccessRights u+rw,g+rw,o-rwx   access rights for written files
outputAccessRightsForDirectories u+rwx,g+rwx,o-rwx   access rights for written directories
possibleControlSampleNamePrefixes ( blood) bashArray possible prefix of control bam if named ${prefix}_${pid}_$mergedBamSuffix
possibleTumorSampleNamePrefixes ( tumor ) bashArray same as possibleControlSampleNamePrefixes
referenceGenome_1KGRef ${path}/hs37d5.fa path reference genome file
REFERENCE_GENOME ${referenceGenome_1KGRef} string  
dbSNP_FILE ${path}/00-All.SNV.vcf.gz path  
MAPPABILITY_FILE ${path}/wgEncodeCrgMapabilityAlign100mer_chr.bedGraph.gz path mappability file
CHROMOSOME_LENGTH_FILE ${path}/chrlengths.txt path  
REPLICATION_TIME_FILE ${path}/ReplicationTime_10cellines_mean_10KB.Rda path replication timing file
GC_CONTENT_FILE ${path}/hg19_GRch37_100genomes_gc_content_10kb.txt path  
GENETIC_MAP_FILE ${path}/genetic_map_chr${CHR_NAME}_combined_b37.txt path impute files
KNOWN_HAPLOTYPES_FILE ${path}/ALL.chr${CHR_NAME}.integrated_phase1_v3. 20101123.snps_indels_svs.genotypes.nomono.haplotypes.gz path impute files
KNOWN_HAPLOTYPES_LEGEND_FILE ${path}ALL.chr${CHR_NAME}.integrated_phase1_v3. 20101123.snps_indels_svs.genotypes.nomono.legend.gz path impute files
GENETIC_MAP_FILE_X ${path}/genetic_map_chrX_nonPAR_combined_b37.txt path impute files
KNOWN_HAPLOTYPES_FILE_X ${path}/ALL_1000G_phase1integrated_v3_chrX_nonPAR_impute.hap.gz path impute files
KNOWN_HAPLOTYPES_LEGEND_FILE_X ${path}/ALL_1000G_phase1integrated_v3_chrX_nonPAR_impute.legend.gz path impute files
outputExecutionDirectory ${path}/exec_${executionTimeString}   path to log files
imputeBaseDirectory ${path}/ path directory for impute files
mergedBamSuffix merged.mdup.bam string A list of all known suffixes for merged bam files. I.e. merged.dupmark.bam, merged.mdup.bam…
mergedBamSuffixList ${mergedBamSuffix} string A list of all known suffixes for merged bam files. I.e. merged.dupmark.bam, merged.mdup.bam…
defaultMergedBamSuffix ${mergedBamSuffix} string The default suffix for merged bam files when they are created by Roddy.
libloc_PSCBS   string path to PSCBS library in R
libloc_flexclust   string path to felxclust library in R