SAMBAMBA-FLAGSTAT(1)

💅 sambamba-flagstat(1) — the flag stats page, bestie edition

okay so this is the manual page for sambamba-flagstat — it's a little tool that pulls stats out of a BAM file's read flags. yes, that sambamba. it's giving "quietly carrying the whole pipeline" energy. 🧚

✨ NAME ✨

sambamba-flagstat — getting flag statistics from a BAM file 🎀

🌸 SYNOPSIS 🌸

sambamba flagstat OPTIONS <input.bam>

🦋 DESCRIPTION 🦋

So what does it actually do? It outputs some statistics drawn from read flags. that's the whole vibe. 💖

The first line contains the numbers of QC-passed and QC-failed reads. After that come pairs of numbers — the former for QC-passed reads, the latter for QC-failed ones. no cap, every line after the first is a little duo like that:

• duplicates
• mapped reads (plus percentage relative to the numbers from the first line)
• reads with is_paired flag set
• paired reads which are first mates
• paired reads which are second mates
• paired reads with proper_pair flag set (plus percentage relative to the numbers of QC-passed/failed reads with is_paired flag set)
• paired reads where both mates are mapped
• paired reads where read itself is unmapped but mate is mapped
• paired reads where mate is mapped to a different chromosome
• the same as previous but mapping quality is not less than 5

👑 OPTIONS 👑

• -t, --nthreads=NTHREADS — specify number of threads to use for BAM decompression. yes bestie, more threads = less waiting around. 💅
• -p, --show-progress — show progressbar in STDERR. it's giving "I want to watch the little bar move". 🍓

heads up: those two options go in OPTIONS, and the input BAM is the <input.bam> positional. don't forget it or the vibe check fails. 😭

k bye, this page is from August 2014 and it's the sambamba-flagstat(1) manual — mwah, love that for us. 🫶✨