Output Files

All the final results will be saved into date_time_core_results directory inside the output folder. core_snp_consensus directory contains the core consensus fasta and vcf files. data_matrix contains all matrices and reports generated during report step.

As the name suggests, data_matrix will contain various matrices that can be queried or plotted for further diagnosing the variant call results. Alternatively, you can run a R script provided inside the data_matrix folder to generate the plots.

Require: ggplot2 and heatmap.3

module load R

Rscript generate_diagnostics_plots.R

Variant Calling: Each sample folder under output directory contains standard variant calling outputs such as clean reads, aligned BAM files, filtered non-core vcf and various stats file.

Core Variants: The final core step results will be moved to *_core_results directory under output directory. There are two results folder, core_snp_consensus and data_matrix. The core SNP vcf and consensus fasta files are stored in core_snp_consensus while the data matrices for useful for variant diagnostics can be found in data_matrix.