samtools-bedcov(1)

okay bestie, welcome to samtools-bedcov(1) from the Bioinformatics tools crew 💖 this is the one that does coverage over regions in a BED file, and yes we're gonna get into every flag.

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🌸 NAME 🌸

samtools bedcov — reports coverage over regions in a supplied BED file. periodt.

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✨ SYNOPSIS ✨

samtools bedcov [options] region.bed in1.sam|in1.bam|in1.cram[...]

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🦋 DESCRIPTION 🦋

So basically: it reports the total read base count — i.e. the sum of per base read depths — for each genomic region specified in the supplied BED file. The regions are output as they appear in the BED file and are 0-based ✨

Columns 1-3 are chrom/start/end as per the input BED file, followed by N columns of coverages (for N input BAMs), then (if given -d), N columns of bases-at-depth-X, then (if given -c) N columns of read counts. literally the whole little column pipeline, iykyk.

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💅 OPTIONS 💅

• -Q, --min-MQ INT — only count reads with mapping quality greater than or equal to INT 🔥 no weak-map reads allowed.
• -g FLAGS — by default, reads that have any of the flags UNMAP, SECONDARY, QCFAIL, or DUP set are skipped. To include these reads back in the analysis, use this option together with the desired flag or flag combination. FLAGS can be specified in hex by beginning with 0x (i.e. /^0x[0-9A-F]+/), in octal by beginning with 0 (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names. [0]

For a list of flag names see samtools-flags(1).

• -G FLAGS — discard any read that has any of the flags specified by FLAGS set. FLAGS are specified as for the -g option. [UNMAP,SECONDARY,QCFAIL,DUP] 👑
• -j — do not include deletions (D) and ref skips (N) in bedcov computation. okay so those little guys are out of the count.
• -d INT — print an additional column, for each file, containing the number of bases having a depth above and including the given threshold. If the option is not used, the extra column is not displayed. The option value must be an integer >= 0. math girlies rise 🧚
• --max-depth INT — specifies the maximum depth used for the mpileup algorithm. If -d is used and is larger then this value will be used instead. Defaults to 2 billion, but smaller values may be used when we do not require an exact count in excessively deep regions and are interested in maximizing speed of results. speed vs exactness, the eternal vibe check.
• -c — print an additional column with the read count for this region. This will be +1 for every read covering the region, not just starting within in. The whole read filtering options -Q, -g and -G options will also have an effect on this count, but -d will not. 💀
• -X — if this option is set, it will allows user to specify customized index file location(s) if the data folder does not contain any index file. Example usage:

samtools bedcov [options] -X <in.bed> </data_folder/in1.bam> [...]  </index_folder/index1.bai> [...]

• -H — okay bestie, the source line here is literally ®copied to the output. and I am not fixing that mysterious ®, I'm just keeping it fr fr. When it is not available, a header is created with field names matching the fields listed in the GA4GH BED specification. The -c and -d options can add further per-file columns named in1.sam_count and in1.sam_depth along with in1.sam_count. 🙈

yes, that ® is really in the source text, and that duplicate in1.sam_count is staying too. no cap.

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🎀 AUTHOR 🎀

Written by Heng Li from the Sanger Institute. 👑

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🌈 SEE ALSO 🌈

samtools(1)

Samtools website: <http://www.htslib.org/>

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later bestie 🫶 this little manual page is from samtools-1.24, dated 9 July 2026 — slay, bye 💖