PARAMETERS.md

nf-ncov-voc Parameters

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