buildSNVtable: M1UK typing pipeline from WGS SNVPhyl M1UK Analysis December...

In phac-nml/wade: Executes molecular typing on contig assemblies

M1UK typing pipeline from WGS SNVPhyl M1UK Analysis December 21 2023, Walter Demczuk & Shelley Peterson

Description

M1UK typing pipeline from WGS SNVPhyl M1UK Analysis December 21 2023, Walter Demczuk & Shelley Peterson

Usage

buildSNVtable(SNVTable, SNPList, pattern_ref)

Arguments

Org_id	Organism to query: GAS, PNEUMO or GONO
variant	M1UK or M1DK - which SNP list should be referenced
locus	Sample number associated with contig.fasta file
curr_work_dir	Start up directory from pipeline project to locate system file structure

Details

GAS emm1 M1UK typing: Use the SNV_Table.csv generated from the SNVphyl Galaxy pipeline, with MGAS5005 (CP000017.2) as a mapping reference. include a known M1UK as a reference so that all SNV positions will be included in Galaxy SNPhyl outputs. This will make LabWareUpload_GAS_M1UK.csv in the local Output directory. Output.csv has SampleNo, SNVprofile and Genotype if SNV profile matches MGAS5005 reference = "Global" genotype if SNV profile has all 27 different = "M1UK" Otherwise = "Intermediate (Number of SNVs vs references)"

Value

A table frame containing the results of the query

phac-nml/wade documentation built on March 16, 2024, 8:32 a.m.