SAMCLIP(1)

📦 version 0.4.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

samclip — bestie, it filters your SAM file so you only keep the alignments that aren't all soft-clipped and hard-clipped. That's the whole vibe. soft and hard clipped alignments get the ✂️ treatment, everything else stays. Periodt.

✨ SYNOPSIS ✨

samclip --ref ref.fa < in.sam > out.sam

Like, that's it. Point it at your reference, feed it a SAM on stdin, catch a SAM on stdout. Iconic behaviour, honestly. 🌈

🦋 USAGE 🦋

In connection with minimap2

Okay so this is the main character pipeline, the one you'll actually use. minimap2 does the aligning, samclip does the filtering, samtools does the sorting, and you get a BAM at the end like a little gift 🎀

minimap2 ref.fa R1.fq R2.fq | samclip --ref ref.fa | samtools sort > out.bam

The pipes are doing SO much work here and I respect them so much. 🫶

🌸 DESCRIPTION 🌸

Filter SAM file for soft & hard clipped alignments.

That's the mission statement, no notes. If an alignment is too clipped, it's out. If it's chillin' with a reasonable clip length, it stays. Simple as. 💅

💅 OPTIONS 💅

  • --help — Prints the help text so you can remind yourself what you're doing. Your little cheat sheet. 📖
  • --version — Prints the version and immediately exits. Short, sweet, no small talk. ✨
  • --ref FASTA — Your reference genome, bestie. It needs a FASTA.fai index — so make sure that index exists or this whole thing is gonna be giving nothing. 🙈
  • --max NUM — The maximum clip length you're willing to allow. Default is 5. Anything longer than this gets filtered. So like, keep it tight. ✂️
  • --invert — Flips the whole thing: outputs the rejected SAM lines and ignores the good ones. Not me being a hater, but this is literally the hater mode of the tool. 💀
  • --debug — Prints verbose debug info to stderr. For when you NEED to know what's going on in there. 🔍
  • --progress N — Prints progress every NUM records. Default is 100000, and none=0 if you want it to shut up entirely. 🤫

🔥 SEE ALSO 🔥

https://github.com/tseemann/samclip

Go. Look. It's right there. 👑

🎀 AUTHOR 🎀

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

Shoutout to Andreas fr fr. 🫡

samclip 0.4.0 — May 2020. That's the version, that's the date, and that's the whole page bestie, mwah 💋 go filter some alignments 💖✨

📦 where this page comes from