This tool has been tested with
python >= 3.9 pysam >= 0.17.0
git clone https://github.com/mjsull/covbamic.git
python covbamic/covbamic.py -b sars_bam_file.primertrimmed.rg.sorted.bam -o output.svg -1 BA.4 -2 BA.5
Where sars_bam_file.primertrimmed.rg.sorted.bam is a sorted and indexed bam file.
-o OUTPUT, --output OUTPUT
output svg file
-b BAM_FILE, --bam_file BAM_FILE
sorted and indexed bam file
-1 VARIANT_1, --variant_1 VARIANT_1
variant 1 (BA.2, BA.4 or BA.5)
-2 VARIANT_2, --variant_2 VARIANT_2
variant 2 (BA.2, BA.4 or BA.5)
-h, --help show this help message and exit
-a, --all List all sites different from reference (as opposed to only sites that differ between the two variants selected).
-m, --all_minor List all sites where the minor allele reaches defined threshold.
-f MINOR_FRACTION, --minor_fraction MINOR_FRACTION
Fraction of reads with minor allele to report (when -m set)
-d MINOR_DEPTH, --minor_depth MINOR_DEPTH
minimum depth to report minor allele site (when -m set)
-p3, --panel3 Draw panel 3.
Example output
