SUBINDEL(1)

🦋 SUBINDEL(1) 🦋

okay so bestie, you've landed on the manual page for subindel — and it lives in section 1 of the manual, aka User Commands, which is the section where the actually-runnable stuff hangs out. come sit with me, this one's short and sweet 🫶

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✨ NAME ✨

subindel — it's a whole toolkit for processing next-gen sequencing data 💅

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🌸 DESCRIPTION 🌸

SubIndel: detect short and long indels. that's the whole vibe. short ones, long ones, it's got both. periodt. 💜

🧚 Usage:

the squiggly braces {} are wrapping the optional little extras — everything else you gotta bring:

subindel -i <SAM file> -g <subread index> -o <output VCF> {-d <expected fragment distance>} {-I <max indel length>} {--paired-end}

so, breaking it all the way down for you:

• -i — hand it your <SAM file>, like, the actual reads 🌸
• -g — point it at your <subread index>, it needs the map bestie 🗺️
• -o — where the <output VCF> goes, name it and claim it ✨
• -d — <expected fragment distance> — optional, curly braces, you know the drill 🎀
• -I — <max indel length> — also optional, also curly braces 💫
• --paired-end — flip this on if your reads are paired-end, it's giving duo energy 👯

🌈 Example:

copy-paste-able, no cap:

subindel -i my_paired_end_reads.SAM -g my_index -o my_result -d 300 -I 200 --paired-end

look at that. my_paired_end_reads.SAM in, my_index doing its thing, my_result out, fragment distance 300, max indel length 200, and --paired-end riding along. iconic. 👑

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👑 AUTHOR 👑

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

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and that's the whole page, bestie! this is subindel version 2.0.3, dated March 2023, and it's the SUBINDEL(1) page you just read. mwah 💖 go detect some indels, you absolute main character 🦋🌸💅