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$ NXF_SYNTAX_PARSER=v2 nextflow run . --help
N E X T F L O W ~ version 25.12.0-edge
Launching `./main.nf` [determined_ritchie]revision: fb7b8319f4
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/variantprioritization 1.0.0dev
------------------------------------------------------
Typical pipeline command:
nextflow run nf-core/variantprioritization -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>
--save_intermediates [boolean]
--panel_id [integer] [default: 0]
--diagnostic_grade_only [boolean]
--ignore_noncoding [boolean]
--pop_gnomad [string] [default: nfe]
--maf_upper_threshold [number] [default: 0.9]
--classify_all [boolean]
--clinvar_ignore_noncancer [boolean]
--vcf2maf [boolean]
--assay [string]
--cpsr_report [string]
--tumor_site [integer] [default: 0]
--tumor_purity [string]
--tumor_ploidy [string]
--cna_analysis [boolean]
--cna_overlap_pct [integer] [default: 50]
--effective_target_size_mb [integer] [default: 34]
--estimate_tmb [boolean]
--estimate_msi [boolean]
--tmb_display [string] [default: coding_and_silent]
--estimate_signatures [boolean]
--min_mutations_signatures [integer] [default: 200]
--all_reference_signatures [boolean]
--include_artefact_signatures [boolean]
--prevalence_reference_signatures [integer] [default: 5]
--include_trials [boolean] [default: true]
--tumor_dp_min [integer] [default: 0]
--tumor_af_min [integer] [default: 0]
--control_dp_min [integer] [default: 0]
--control_af_max [integer] [default: 1]
--tumor_only [boolean]
--pon_vcf [string]
--exclude_pon [boolean]
--exclude_likely_hom_germline [boolean]
--exclude_likely_het_germline [boolean]
--exclude_dbsnp_nonsomatic [boolean]
--exclude_nonexonic [boolean]
--maf_gnomad_nfe [number] [default: 0.002]
--maf_gnomad_fin [number] [default: 0.002]
--maf_gnomad_asj [number] [default: 0.002]
--maf_gnomad_oth [number] [default: 0.002]
--maf_gnomad_amr [number] [default: 0.002]
--maf_gnomad_afr [number] [default: 0.002]
--maf_gnomad_eas [number] [default: 0.002]
--maf_gnomad_sas [number] [default: 0.002]
--maf_gnomad_global [number] [default: 0.002]
--filter_haplotypecaller [string] [default: -i\'FORMAT/DP>10\]
--filter_deepvariant [string] [default: -i\'FORMAT/DP>10\]
--filter_strelka_variants [string] [default: -i\'FORMAT/DP>10\]
--filter_freebayes_germline [string] [default: -i\'FORMAT/DP>10\]
--filter_mutect2 [string] [default: -i\'FORMAT/DP>10\]
--filter_freebayes_somatic [string] [default: -i\'FORMAT/DP>10\]
--filter_strelka_indels [string] [default: -i\'FORMAT/DP>10\]
--filter_strelka_snvs [string] [default: -i\'FORMAT/DP>10\]
--vep_n_forks [integer] [default: 4]
--vep_buffer_size [integer] [default: 500]
--vep_gencode_all [boolean] [default: true]
--vep_pick_order [string] [default: mane_select,mane_plus_clinical,canonical,biotype,ccds,rank,tsl,appris,length]
--vep_no_intergenic [boolean]
help message of that parameter will be printed.
or `--helpFull`.
Input/output options
--input [string] Path to comma-separated file containing information about the samples in the experiment.
--outdir [string] The output directory where the results will be saved. You have to use absolute paths to storage on
Cloud infrastructure.
--email [string] Email address for completion summary.
--multiqc_title [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified.
Reference genome options
--genome [string] Name of iGenomes reference.
Reference database options
--vep_cache [string] [default: s3://annotation-cache/vep_cache/]
--vep_cache_version [integer] [default: 113]
--pcgr_download [boolean] [default: true]
--pcgr_bundleversion [integer] [default: 20250314]
--pcgr_database_dir [string]
Generic options
--multiqc_methods_description [string] Custom MultiQC yaml file containing HTML including a methods description.
--help [boolean, string] Display the help message.
--help_full [boolean] Display the full detailed help message.
--show_hidden [boolean] Display hidden parameters in the help message (only works when --help or --help_full are provided).
!! Hiding 21 param(s), use the `--showHidden` parameter to show them !!
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* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/variantprioritization/blob/master/CITATIONS.md