This repository is for the scripts to find reads containing partial leader sequence in the SARS-CoV-2 genome. The scripts here are writen in bash and awk for use on a linux system.

The scripts take a mapped SAM/BAM file and look for reads with the sequence motif GTAGATCTGTTCTCT, which occurs at the 3' end (nucleotides 52-67) of the SARS-CoV-2 leader.

You will need to install samtools on the system for the scripts to work correctly. On Debian this is done by: sudo apt install samtools

The script will output a BAM and SAM file containing only the reads with the above motif. The script will also produce a summary csv file on the total number of reads, the number of reads containing the leader, how many of those reads belong to the 5'UTR and then ratios of leader reads between the 5' UTR and subgenomic regions.

It will also produce a csv file using samtools depth to show the coverage at each position at the specified Q value.