Utility scripts and visualization

Binning of haplosets

See https://github.com/maxibor/floria-strainer (developed by Maxime Borry at Max Planck) if you’re interested in creating larger haplosets by binning haplosets using coverages.

Vartig-utils for mapping vartigs

See the repository (https://github.com/bluenote-1577/vartig-utils) if you’re interested in comparing vartigs across samples (but using the same VCF file).

Visualization scripts

floria comes with some utility scripts that are useful for visualizing results. These scripts can be found in floria/scripts in floria’s github repository: https://github.com/bluenote-1577/floria.

Requirements

All scripts below use python3 and require the following standard dependencies (can be installed by pip install ...)

  1. matplotlib

  2. numpy

  3. natsort (https://pypi.org/project/natsort/)

visualize_vartigs.py

Very useful script for quickly visualizing output vartigs.

floria visualization example.

Each line is a vartig passing certain thresholds. The top plot is colored by the alternate allele ratio of the vartig, i.e. what fraction of the vartig’s alleles are alternate? For a good phasing, you would expect the coverage and allele ratios of vartigs from the same strain to be similar.

#visualize vartigs only if HAPQ >= 15, COV >= 50, LENGTH >= 10000
python visualize_vartigs.py floria_out_dir/contig1/contig1.vartigs -q 15 -c 50 -l 10000

haplotag_output_dir.py

If you want to visualize floria’s output phasings in the IGV, use this script. This adds a HP:i tag to the same BAM file that was input to floria for all reads in contigs that were successfully phased by floria.

floria -b my_bam_file.bam -v some.vcf -r ref.fa
# floria_out_dir is output directory

python haplotag_output_dir.py -d floria_out_dir/ -b my_bam_file.bam -o output_prefix

#haplotagged bam file with HP:i flags.
ls output_prefix.bam

For an example of how to visualize this output bam file, see Tutorial 1: running floria and visualizing its outputs.

haplotag_bam.py

This script does the same thing as haplotag_output_dir.py, but you can specify exactly which contig to haplotag.