Recombination

A collection of scripts for the detection and visualisation of recombinants from SARS-CoV-2 sequence data.

Visualisation

To run the visualisation script, just call the script with the directory containing your FASTA or VCF files as its first argument from the visual directory, e.g.:

~/recombination/visual$ ./visual.sh ../data

An output directory can be provided as an optional second argument to the script (default dir is recombination/output).

In case you call visual.sh on a FASTA file(s) the script will try to run covSonar on the file(s) to generate a VCF file for visualisation.

Since covSonar does not provide the allel frequency field in its VCF output, the allel frequency is estimated from the provided AC and AN fields from the VCF file.

The VCF files are then annotated using snpEff and formatted with SnpSift for later visualization in the Heatmap.R script.

NOTE: Both covSonar and snpEff use the SARS-cov2 isolate Wuhan-Hu-1 complete genome as reference for variant detection.

NEW:

• Added support for multifasta files, eg.: ~/recombination/visual$ ./visual.sh -m my_multi_fasta_file.fasta
• Added support for metadata sheets (tsv), e.g.: ~/recombination/visual$ ./visual.sh -m my_multi_fasta_file.fasta -t my_metadata_file.tsv. If provided the heatmap will sort sequences by the date associated with them in the metadata file.
• The script now makes heatmaps for all sequences merged into one VCF, so you get the different allel frequencies, but also a heatmap with all sequences seperately where allel frequency is either 1 or 0.
• Genomemap plots are currently not working. Please use the code from branch old to generate these plots. NOTE: Everything listed under NEW is not available there.