nf-core/dragen/germline @ 0.0.0-c4ed7fd
Summary
The DRAGEN DNA Germline Pipeline accelerates the secondary analysis of NGS data by harnessing the tremendous power available on the DRAGEN Platform. The pipeline includes highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. In addition to haplotype variant calling, the pipeline supports calling of copy number and structural variants as well as detection of repeat expansions and targeted calls.
Get started
Add the following snippet to your workflow script to include this module.
include { DRAGEN } from 'nf-core/dragen/germline'
License
MIT License
Name
|
DRAGEN |
|---|
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
input
file
|
FASTQ (may be gzipped), ora, BAM or CRAM files *.{fastq,fq,ora,bam,cram}{,.gz}
|
sex
string
|
Sample's sex. Recognize options: male, female, none, auto |
checkfingerprint_expected_vcf
file
|
Input expected genotypes (VCF) for checkfingerprint comparison *.vcf
|
|---|
cnv_combined_counts
file
|
Specify combined PON file *.combined.counts.txt.gz
|
|---|
cnv_exclude_bed
file
|
Regions to exclude for CNV processing *.bed
|
|---|
cnv_population_b_allele_vcf
file
|
CNV population SNP input VCF file *.vcf
|
|---|
cnv_segmentation_bed
file
|
Intervals to limit segmentation to *.bed
|
|---|
cnv_target_bed
file
|
CNV target BED file *.bed
|
|---|
cram_reference
file
|
Reference file in FASTA format (only used for decompression) *.{fasta,fa}
|
|---|
dbsnp
file
|
Variant annotation database VCF (or .vcf.gz) file *.vcf{,.gz}
|
|---|
fastqc_adapter_file
file
|
FASTA file containing adapter sequences *.{fasta,fa}
|
|---|
fastqc_kmer_file
file
|
FASTA file containing kmers of interest *.{fasta,fa}
|
|---|
ora_reference
directory
|
Path to the directory that contains the compression reference and index file |
|---|
qc_coverage_region
file
|
bed files to report coverage on, max 3 *.bed
|
|---|
qc_cross_cont_vcf
file
|
Variant file (.vcf/.vcf.gz) with population allele frequencies to estimate sample contamination *.vcf{,.gz}
|
|---|
ref_dir
directory
|
Directory with reference and hash tables |
|---|
repeat_genotype_ref_fasta
file
|
FASTA file containing repeat genotypes *.{fasta,fa}
|
|---|
repeat_genotype_specs
file
|
Repeat variant catalog file |
|---|
sv_call_regions_bed
file
|
BED file containing the set of regions to call (optionally gzip or bgzip compressed) *.bed{,.gz}
|
|---|
sv_exclusion_bed
file
|
BED file containing the set of exclusion regions for SV calling (optionally gzip or bzip compressed) *.bed
|
|---|
sv_forcegt_vcf
file
|
Specify a VCF of structural variants for forced genotyping, meaning these variants will be scored and emitted in the output VCF even if not found in the sample data. These variants will be merged with any additional variants discovered directly from the sample data. *.vcf
|
|---|
sv_systematic_noise
|
|---|