MAQ.PL(1)

💖 MAQ.PL 💖

okay bestie, listen — this is the manual page for maq.pl, a User Commands situation, section 1 of the manual. it's the little helper script that tags along with maq and does the running-around so you don't have to 🏃♀️✨

✨ NAME ✨

maq.pl — helper script for maq 🫶

🌸 SYNOPSIS 🌸

maq.pl <command> [options] <input> [...]

like… you give it a command, you give it some options, you give it your inputs, and it goes. that's the whole vibe. 🎀

🦋 DESCRIPTION 🦋

helper script for maq 💅

Version: 0.4.7

that's it. that's the description. she's a helper. she helps. iconic behaviour, no notes. 👑

💅 OPTIONS. 💅

these aren't your regular flags, bestie — these are the commands you can hand to maq.pl. pick one, she's got you 💜

• easyrun — a simple pipeline for a small dataset. tiny data? easy run. 🍓
• demo — a demonstration of maq functionalities — and heads up, it's for SE only, so don't come at her with paired-end, she said what she said. 🙈
• SNPfilter — filter SNPs. yes, that's the whole job. slay. 🔥
• statmap — extract statistics from the error output of maq map. she reads the mess so you get the numbers. ✨
• chrpt2snp — convert dbSNP's chr_rpt file to a .snp file. format glow-up, no cap. 🌈
• ucsc2snp — convert UCSC's SNP dump to a .snp file. same energy, different source. ⭐
• fastq2bfq — convert fastq in batch. batch mode because doing it one at a time is not the move. 🧚
• cat2pair — convert paired end reads format. pairing them up like it's a group chat 💬
• sv — call structural variations. big structural drama, she finds it. 👑
• indelpe — post-processing of indelpe output. the cleanup era. 🎀

💖 AUTHOR 💖

The program was written by Heng Li <lh3@sanger.ac.uk>. 🫶

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

and that's the whole page, bestie!! 🎉 this was maq.pl 0.7.1, dated December 2015 — genuinely a whole era ago, and she's still here helping. periodt. 💅✨🦋