nf-core/rarevariantburden
Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.
Define where the pipeline should find input data and save output data.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Define different pipeline parameters.
Joined called and VQSR applied vcf file from the case cohort. If you already have splitted joined called VCF file by chromosome, you need to put ‘NA’ in here and provide the splitted VCF file list in the ‘caseVCFFileList’ parameter.
string
One column text file containing list of samples, one sample ID per line.
string
Input files needed for the pipeline from the control dataset, for now we support 3 gnomAD datasets as control, gnomADv2exome, gnomADv4.1exome, gnomADv4.1genome. You need to download these datasets from our Amazon AWS s3 bucket: s3://cocorv-resource-files/
string
Reference genome build version, allowed values are “GRCh37”, “GRCh38”. Default value: “GRCh38""
string
GRCh38
gnomAD version, allowed values are “v2exome”, “v4exome”, “v4genome” (for GRCh37 data use “v2exome”, for GRCh38, use “v4exome” or “v4genome”). Default value: “v4exome""
string
v4exome
Bed file containing good coverage positions from case vcf files where 90% samples have coverage >= 10.
string
NA
List of chromosomes you want to analyze, you can test only for chromosome 21 and 22, in that case, it will be “21 22”
string
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
An optional R file with functions or a tab separated two column text file defining the variants of interest
string
NA
An optional JASON file to provide extra parameters to the custuomized file variantGroupCustom
string
NA
A one column file without the header listing all required annotations used in variant filtering. AC AN annotations from ACANConfig will be added automatically
string
NA
Optional options for CoCoRV module
string
NA
The column header used to pull Gene name from annotation file, default: ‘Gene.refGene’, for VEP, use ‘SYMBOL’
string
Gene.refGene
A one column file specifying the variants to be included, it will also include variants specified in variantExcludeFile
string
NA
Batch size for CoCoRV module
integer
10000
The folder path containing CoCoRV R package
string
/opt/cocorv/
The maximum of the alternate allele frequency, for gnomADv2exome, we used 0.0001, for gnomADv4.1genome and v4.1exome, we used 0.0005
number
0.0005
The maximum missingness allowed for a variant
number
0.1
A specified variant group to use for test or a self defined function to define the variants of interest
string
annovar_pathogenic
The minimum REVEL score for pathogenic missense variants
number
0.65
The p-value threshold to detect high LD variants in control
number
0.05
Bed file containing good coverage positions from gnomAD control files where 90% samples have coverage >= 10.
string
null/coverage10x.bed.gz
The reference genome file
string
null/reference.fasta.gz
If you split you joined called VCF file by chromosome, you can supply the VCF file list here, the list needs to be in csv format (comma seperated), the column headers are chr,vcf. Then you need to list the chromosome number and the coresponding vcf file for that chromosome.
string
NA
Pre-normalized case VCF files, you can use the pre-normalized case VCF files to skip the normalization steps in the pipeline, the list needs to be in csv format (comma seperated), the column headers are chr,vcf,index. Then you need to list the chromosome number and the coresponding vcf file and .tbi file for that chromosome.
string
NA
Pre-annotated case VCF files, you can use the pre-annotated case VCF files to skip the annotation steps in the pipeline, the list needs to be in csv format (comma seperated), the column headers are chr,vcf,index. Then you need to list the chromosome number and the coresponding vcf file and .tbi file for that chromosome.
string
NA
GDS converted genotype case VCF files, you can use it to skip the genotype GDS conversion steps in the pipeline, the list needs to be in csv format (comma seperated), the column headers are chr,gds. Then you need to list the chromosome number and the coresponding gds file for that chromosome.
string
NA
GDS converted annotated case VCF files, you can use it to skip the annotation GDS conversion steps in the pipeline, the list needs to be in csv format (comma seperated), the column headers are chr,gds. Then you need to list the chromosome number and the coresponding vcf file for that chromosome.
string
NA
GDS converted genotype control VCF files from gnomAD control data
string
null/controlGenotypeGDS.csv
GDS converted annotated control VCF files from gnomAD control data
string
null/controlAnnotationGDS.csv
Define different pipeline parameters for annotating with ANNOVAR and VEP.
Resource folder for the annotation tool Annovar, you can download this folder from our Amazon AWS s3 bucket: s3://cocorv-resource-files/annovarFolder/
string
Resource folder for the annotation tool VEP, you can download this folder from our Amazon AWS s3 bucket: s3://cocorv-resource-files/vepFolder/
string
Annotation options for Annovar, default: ‘refGene,gnomad211_exome,revel’
string
refGene,gnomad211_exome,revel
Annotation options for Annovar, default: ‘g,f,f’
string
g,f,f
If you want to run only VEP annotation, you need to put “VEP” for this parameter, if you want both annovar and vep, you need to put “ANNOVAR_VEP”. Default: “ANNOVAR”, meaning only run Annovar.
string
ANNOVAR
VEP annotation parameters, list of VEP plugins to run
string
AM,SPLICEAI,LOFTEE,CADD
Annotation options for Annovar
string
NA
Annotation options for Annovar
string
NA
Define different pipeline parameters for predicting ancestry.
File containing estimation of the population/ethnicity of case samples using gnomAD classifier, optional, if not specified nextflow app will estimate the population using gnomAD classifier.
string
NA
The files containing variant positions needed for gnomAD ancestry prediction classifier
string
null/ancestry/hail_positions.chr.pos.tsv
Files needed for gnomAD ancestry prediction classifier
string
null/ancestry/gnomad.pca_loadings.ht/
Files needed for gnomAD ancestry prediction classifier
string
null/ancestry/gnomad.RF_fit.onnx
Define different pipeline parameters for sex-stratified analysis.
If you want to do sex stratified analysis, need to put “true” here. Default: “false”
boolean
a file with header, 1st column is ID, and must have a column named “Sex”. The sex is coded either as Male/Female, 1/2, or XY/XX, NA means missing
string
NA
Define different pipeline parameters for post checking the CoCoRV results by generating variant sample info for top K genes.
Top K genes for generating variant-sample information for each gene
integer
1000
Case or control for which top K genes need to be examined
string
case
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email address for completion summary, only when pipeline fails.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Send plain-text email instead of HTML.
boolean
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/
Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string