CONVERT2BED(1)

🎀 convert2bed — the manual page, but make it a group chat 🎀

okay bestie, sit down, hydrate, because we're about to talk about convert2bed, aka the glow-up machine that takes your dusty genomics formats and turns them into BED. this is the convert2bed(1) manual page, and yes it is iconic. 💅

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✨ NAME ✨

convert2bed — manual page for convert2bed 2.4.42+dfsg

literally that's it, that's the name, no notes. 🫶

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🌸 DESCRIPTION 🌸

convert2bed

version: 2.4.42

author: Alex Reynolds

Usage:

$ convert2bed --input=fmt [--output=fmt] [options] < input > output

okay so here's the whole vibe: this tool converts BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF and WIG genomic formats into BED or BEDOPS Starch (that's compressed BED, for the uninitiated — iykyk). 🔥

and the input? it can be a regular file, OR standard input piped in using the hyphen character ('-'). the way that works is just:

$ some_upstream_process ... | convert2bed --input=fmt - > output

ate. no crumbs. 🍓

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🌈 Input (required): 🌈

• --input=[bam|gff|gtf|gvf|psl|rmsk|sam|vcf|wig] (-i <fmt>) — the genomic format of your input file. required, bestie, you cannot skip this one, it is the whole personality of the command. 💖

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🦋 Output: 🦋

• --output=[bed|starch] (-o <fmt>) — the format of your output file, either BED or BEDOPS Starch. it's optional, and the default is BED. 🎀

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💜 Other processing options: 💜

• --do-not-sort (-d) — do not sort BED output with sort-bed. heads up though: this is not compatible with --output=starch. 🚫
• --max-mem=<value> (-m <val>) — sets aside <value> memory for sorting BED output. for example, <value> can be 8G, 8000M or 8000000000 to specify 8 GB of memory. the default is 2G. 🧚
• --sort-tmpdir=<dir> (-r <dir>) — optionally sets [dir] as the temporary directory for sort data, when used in conjunction with --max-mem=[value], instead of the host's operating system default temporary directory. (yes, [dir] and [value] are literally how the original writes them, we keep it exact around here 💅)
• --starch-bzip2 (-z) — used with --output=starch, the compressed output explicitly applies the bzip2 algorithm to compress intermediate data. the default is bzip2. 🫶
• --starch-gzip (-g) — used with --output=starch, the compressed output applies gzip compression on intermediate data. 🌸
• --starch-note="xyz..." (-e "xyz...") — used with --output=starch, this adds a note to the Starch archive metadata. cute little annotation moment. ✨
• --help | --help[-bam|-gff|-gtf|-gvf|-psl|-rmsk|-sam|-vcf|-wig] (-h | -h <fmt>) — show the general help message (or detailed help for a specified input format). yes you can ask for help about a specific format, main character behavior honestly. 👑
• --version (-w) — show application version. ⭐

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💫 SEE ALSO 💫

The full documentation for convert2bed is maintained as a Texinfo manual. If the info and convert2bed programs are properly installed at your site, the command

info convert2bed

should give you access to the complete manual. go read it, it's giving ✨ thorough ✨. no cap. 🙈

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ok that's the whole page bestie, you're officially fluent in convert2bed. periodt. 💖

convert2bed 2.4.42+dfsg — that's the source/version, and this lovely little page is dated August 2025. mwah. bye bye! 🎀💅🌈