Often one of the first descriptive statistics of interest for a .bam file is the total number of alignments included in the BAM file. An alignment is where a read from a next-generation sequencing approach maps to the reference genome. There are a few ways of calculating the total number of mapped, unmapped, and overall number of alignments, but in my opinion samtools provides the most powerful and efficient means of doing this. Here are some simple example scripts to count total alignments and total reads in a bam file.
Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.