raredisease

Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa', 'bwameme' and 'sentieon'.

Memory allocated for mbuffer in megabytes (MB) (used by bwameme and bwafastalign)

Discard trimmed reads shorter than the given value

Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa' and 'sentieon'.

Subsample mitochondria based on fraction of reads or number of reads

Expected coverage to subsample mt alignment to, when mt_subsample_approach is set to fraction

Expected number of reads to subsample mitochondria to, when mt_subsample_approach is set to reads

Subsampling seed used to influence which subset of mitochondrial reads is kept. Used when mt_subsample_approach is set to fraction

Specifies whether duplicates reads should be removed prior to variant calling.

Number of threads allocated for sorting alignment files (used by bwameme and bwafastalign)

Specifies which analysis type for the pipeline- either 'wgs', 'wes' or 'mito'. This changes resources consumed and tools used.

Specifies whether to generate a concatenated VCF file containing both nuclear & mitochondrial snv calls

After aligning the reads to a reference, remove alignments to alt contigs using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM).

After aligning the reads to a reference, extract alignments from specific regions/contigs and restrict the analysis to those regions/contigs.

Allele frequency threshold for mitochondrial variants. Variants with an AF above this threshold will be treated as homoplasmic and assigned a 1/1 genotype. Range 0-1.0.

Method selection for ngs-bits samplegender

Specifies the platform on which the reads were sequenced.

Can be specified as RNAME[:STARTPOS[-ENDPOS]]. Multiple regions should be seperated by space

Specifies whether to run mitochondrial analysis for wes samples

Specifies whether to run rtgtools' vcfeval

Specifies whether to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno

Specifies whether to generate and publish all (unfiltered) alignment files as cram instead of bam

Specifies whether to generate and publish alt-filtered alignment files as cram instead of bam. Requires exclude_alt to be set to true.

Number of intervals to split your genome into (used to parallelize annotations)

Skip the split multiallelics step in SNV calling.

Disable specified subworkflows.

Disable specified tools.

File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs.

File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs.

Specify the version of the VEP cache provided to the --vep_cache option.

Display the help message.

Display the full detailed help message.

Path to a file containing internal ids and alternative ids in tab separated format. Will replace the internal id with the alternative id in the report. For more info check, docs.seqera.io/multiqc/reports/customisation#sample-name-replacement

Display hidden parameters in the help message (only works when --help or --help_full are provided).

Path to the samplesheet file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

end of heavy strand origin

start of heavy strand origin

Minimum memory required to build HISAT2 index with splice sites and exons. If available memory is below this threshold, a simpler index is built without splice sites.

end of light strand origin

start of light strand origin

length of mitochondrial genome

minimum number of bases a non-split read must span either side of a breakpoint to be considered in the heteroplasmy count

the maximum deviation a given set of split read breakpoints can have to be considered within the same cluster

minimum number of reads supporting a cluster

the maximum size of the gap between fragments of a split read for the split read to be considered as potentially spanning a deletion

the minimum size of the gap between fragments of a split read for the split read to be considered as potentially spanning a deletion

depth to subsample fastq files to before running mitosalt

alignment e-value cutoff

filter split reads if both fragments fall within the regions at the start and end to avoid pseudo-gapped alignments due to a circular genome

basepairs flanking a deletion

detected heteroplasmy threshold

the maximum distance of a paired read from its split counterpart for paired support to be considered positive

alignment score cutoff

maximum size of deletions tolerated, beyond which they are reclassified as potential duplications in the reverse orientation

the maximum length of unmapped distance between two fragments of a split read

minimum number of bases in a split read fragment for the read to be considered as potentially spanning a deletion

fraction for dominant fraction for saltshaker classification

spatial clustering radius for saltshaker grouping

high heteroplasmy threshold for saltshaker classification

threshold for multiple saltshaker classification

heteroplasmy threshold for background noise

The amount to pad each end of the target intervals to create bait intervals.

Directory for pre-built bwa index.

Directory for pre-built bwa-fastalign index.

Directory for pre-built bwamem2 index.

Directory for pre-built bwameme's learned index.

Path to the directory containing pre-scored CADD indel annotations.

Path to the directory containing cadd annotations.

Path to FASTA genome index file.

Path to FASTA genome file.

A file containing the path to models produced by GATK4 GermlineCNVCaller cohort.

Name of iGenomes reference.

Path to the gnomad tab file with allele frequencies.

Path to the index file for the gnomad tab file with allele frequencies.

Do not load the iGenomes reference config.

Path to the interval list of the genome (autosomes, sex chromosomes, and mitochondria).

Path to the interval list of the Y chromosome.

Path to known dbSNP file.

Path to known dbSNP file index.

Local directory base for genome references that map to the config.

Path to a bgzipped BED file restricting Manta SV calling to specific regions (e.g. primary chromosomes). Only applied for WGS; for WES, Manta always uses target_bed instead.

Tabix index for the file supplied via --manta_call_regions.

Name of the mitochondrial contig in the reference fasta file

Path to sentieon machine learning model file.

File with mobile element references

File with mobile element allele frequency references

Path to mitochondrial FASTA genome file.

Path to a BED file containing PAR regions (used by deepvariant).

Directory containing the ploidy model files

Interval list file containing the intervals over which read counts are tabulated for CNV calling

File with gene ids that have reduced penetrance. For use with genmod

Vcf used for evaluating variant calls.

A BED file with regions of interest used in sambamba depth.

Path to a file containing internal ids and customer ids in csv format.

If generated by the pipeline save the required indices/references in the results directory.

MT rank model config file for genmod.

SNV rank model config file for genmod.

SV rank model config file for genmod.

Directory for pre-built sdf index. Used by rtg/vcfeval

Path to the genome dictionary file

Databases used for structural variant annotation in chrA-posA-chrB-posB-type-count-frequency format.

Databases used for structural variant annotation in vcf format.

Path to directory for target bed file.

Path to variant catalog file

Path to vcf2cytosure blacklist file

Path to a VCF file containing annotations.

Path to the vcfanno lua file.

Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.

Path to the vcfanno toml file.

Path to vep's cache directory.

Path to the file containing HGNC_IDs of interest on separate lines.

Path to a bed-like file exported by scout, which contains HGNC_IDs to be used in filter_vep.

Databases used by both named and custom plugins to annotate variants.

Path to a BED file containing markers used by verifybamid2.

Path to mean matrix file of genotype matrix. Used by verifybamid2.

Path to UD matrix file from SVD result of genotype matrix. Used by verifybamid2.

Interval in the reference that will be used in the software. Used only by sentieon.

Bin size for CNVnator

Option for selecting the PCR indel model used by Sentieon Dnascope.

Specifies the variant caller to use - available options are 'deepvariant' and 'sentieon'.

Specifies the variant types for sentieon variant caller.