Workflows

Using:

• vadr annotation (virus model must be selected in options)
• vardict variant caller
• coverage depth Provides summarizing files:
• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only

SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).

PAIRED-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT THE MOST ADAPTED VADR MODEL for annotation (see vadr parameters).

Using:

• vadr annotation (virus model must be selected in options)
• vardict variant caller
• coverage depth Provides summarizing files:
• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only

Using:

• vadr annotation (virus model must be selected in options)
• vardict variant caller
• coverage depth Provides summarizing files:
• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)

Using:

• vadr annotation (virus model must be selected in options)
• vardict variant caller
• coverage depth Provides summarizing files:
• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)