nf-core/phaseimpute
A bioinformatics pipeline to phase and impute genetic data
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string
^\S+\.csv$
Region of the genome to use (optional: if no file given, the whole genome will be used). The file should be a comma-separated file with 3 columns, and a header row.
string
^\S+\.csv$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Should the panel VCF files be renamed to match the reference genome (e.g. ‘chr1’ -> ‘1’)
boolean
Maximum number of contigs name to print before resuming (i.e. show only subset and add ’…’ at the end).
integer
4
Comma-separated list of samples to remove from the reference panel. Useful for benchmarking purposes.
string
^([a-zA-Z0-9]+)(,[a-zA-Z0-9]+)*$
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Step(s) to run.
string
Imputation tool to use.
string
Arguments for the simulation mode
Depth of coverage for the simulated data
integer
1
Genotype position to use to simulate the data
string
^\S+\.(csv|tsv|txt)$
Arguments for the preparation of the reference panel
Path to the reference panel or csv file with the list of panels
string
^\S+\.(csv|tsv|txt)$
Should the reference panel be phased
boolean
true|false
Should the reference panel be normalized
boolean
true|false
Should the allele frequency for each variant (AC/AN fields necessary for Glimpse1 and the validation step) be computed using VCFFIXUP tool. This can be necessary if the fields are absent from the panel or if samples have been removed.
boolean
Model type to use for GLIMPSE2_CHUNK
string
Arguments for the imputation steps
Maximal number of individuals per batch for imputation.
integer
100
Path to comma-separated file containing tab-separated files with the genomic chunks to be used for imputation.
string
^\S+\.csv$
Seed for random number generation in Stitch and Quilt software
integer
1
Arguments for the concordance analysis of the imputed data
Path to comma-separated file containing information about the samples truth files in the experiment.
string
^\S+\.csv$
User-defined allele count bins used for rsquared computations.
string
0 0.01 0.05 0.1 0.2 0.5
^(\d+(\.\d+)? )+(\d+(\.\d+)?)$
Minimum genotype likelihood probability P(G|R) in validation data. Set to zero to have no filter, if using gt-validation
number
0.9
^\d+(\.\d+)?$
Minimum coverage in validation data. If FORMAT/DP is missing and -min_val_dp > 0, the program exits with an error. Set to zero to have no filter of if using –gt-validation
integer
5
^\d+$
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Path to FASTA index genome file.
string
^\S+\.fn?a(sta)?(\.gz)?\.fai$
Path to gmap genome file.
string
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
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
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Optional two-column sample renaming file. First column a set of patterns, second column a set of corresponding replacements. Passed via MultiQC’s --replace-names
option.
string
Optional TSV file with headers, passed to the MultiQC —sample_names argument.
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/phaseimpute/
Arguments to customize QUILT run
Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd.
integer
10000
Number of generations since founding of the population to use for imputation.
integer
100
Arguments to customize STITCH run
Path to comma-separated file containing tab-separated files describing the variable positions to be used for imputation. Refer to the documentation for the --posfile
argument of STITCH for more information.
string
^\S+\.(csv|tsv|txt)$
Number of ancestral haplotypes to use for imputation. Refer to the documentation for the --K
argument of STITCH for more information.
integer
2