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
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 |