Flaggstat

Flaggstat is a utility within the SAMtools software suite used to summarize alignment data from BAM or SAM files. It analyzes the flag field of each read and produces a concise report describing the composition of reads in the alignment, such as how many reads were mapped and how many were paired. The name Flaggstat is a variant spelling; the canonical command in SAMtools is flagstat.

The program reads an input BAM/SAM file and outputs several lines, each reporting counts for a category. Typical categories include total reads, mapped reads, paired reads in sequencing, read1, read2, properly paired reads, reads with their mate mapped, and reads where the mate maps to a different chromosome. Some versions also report singletons and two primary alignments. The exact set of categories and formatting can vary slightly between SAMtools releases.

Flaggstat is widely used as a quick quality-control step before downstream analyses. It does not provide per-base metrics or coverage information, but it offers a fast snapshot of alignment success and library characteristics, helping to identify issues such as low mapping rates or imbalanced pairing.

Usage is straightforward: run samtools flagstat <alignment.bam>. In newer SAMtools versions or with large datasets, the -@ option can be used to enable multithreading, and the exact output format may differ across releases. Because Flaggstat relies on the SAM flag field, its accuracy depends on proper flagging during alignment and any QC filtering applied to the BAM. For more detailed statistics, users may supplement it with additional tools in the SAMtools suite.