Input/Output parameters
Define where the pipeline should find input data and save output data.
--startdate
Starting date to extractdataset (yyyy-mm-dd).--enddate
Starting date to extractdataset (yyyy-mm-dd).
Quality Control parameters (
BBMap
)
Define where the pipeline should find input data and save output data.
--maxns
Reads shorter than this after trimming will be discarded.--minlength
Reads shorter than this after trimming will be discarded.
Mapping parameters (
MiniMap2
/BWA
)
Define where the pipeline should find input data and save output data.
--ref
Instead of indexing the reference file in the again, the prefix of previously-created reference index files can be used.--keep_min_map_quality
Minimum mapping quality of covid reads to keep--remove_min_map_quality
Minimum mapping quality of the human reads to remove
Variant Calling parameters (
Freebayes
/iVar
)
Define where the pipeline should find input data and save output data.
--ploidy
Sets the ploidy for the analysis--var_MinFreqThreshold
Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position.--var_MinDepth
Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position.--mpileupDepth
Mpileup depth for iVar (although undocumented in mpileup, setting to zero removes limit).--var_FreqThreshold
Frequency threshold for consensus variant.--var_MinVariantQuality
Minimum mapQ to call variant.--lower_ambiguityFrequency
Variants with frequency less that this will be discarded.--upper_ambiguityFrequency
Substitution variants with frequency less than this will be encoded with IUPAC ambiguity codes