amplicon_cov

This script computes per amplicon relative coverage for a batch of samples. It outputs a .csv with samples in the rows, first column is sample name and 98 other columns are amplicons.
It needs a bedfile of primers, a .tsv to list the samples (like /cluster/project/pangolin/working/samples.tsv) and a directory where to find the aligned samples (like /cluster/project/pangolin/working/samples/).
Optionally outputs plots.

Example of usage:

If we want to analyze coverage of samples in batch HY53JDRXX, with primers info in 'articV3primers.bed', we first need to create a tsv list of samples:

grep 20210122_HY53JDRXX /cluster/project/pangolin/working/samples.tsv > samples20210122_HY53JDRXX.tsv

Then to compute coverages while plotting and with verbose, outputting into '20210122out' (I think you need to create directory first):

python ./amplicon_covs.py -pv -s samples20210122_HY53JDRXX.tsv -r articV3primers.bed -o 20210122out/