sort — bedtools 2.31.0 documentation

# sort

The `bedtools sort` tool sorts a feature file by chromosome and other criteria.

## Usage and option summary

Usage:

    bedtools sort [OPTIONS] -i <BED/GFF/VCF>

(or):

    sortBed [OPTIONS] -i <BED/GFF/VCF>

Option | Description
--- | ---
-sizeA | Sort by feature size in ascending order.
-sizeD | Sort by feature size in descending order.
-chrThenSizeA | Sort by chromosome (asc), then by feature size (asc).
-chrThenSizeD | Sort by chromosome (asc), then by feature size (desc).
-chrThenScoreA | Sort by chromosome (asc), then by score (asc).
-chrThenScoreD | Sort by chromosome (asc), then by score (desc).
-g | Define sort order by order of tab-delimited file with chromosome names in the first column.
-faidx | Define sort order by order of tab-delimited file with chromosome names in the first column. Sort by specified chromosome order.

## Default behavior

By default, `bedtools sort` sorts a BED file by chromosome and then by start position in ascending order.

For example:

    cat A.bed
    chr1 800 1000
    chr1 80  180
    chr1 1   10
    chr1 750 10000

    sortBed -i A.bed
    chr1 1   10
    chr1 80  180
    chr1 750 10000
    chr1 800 1000

## Optional sorting behavior

`bedtools sort` will also sort a BED file by chromosome and then by other criteria.

For example, to sort by chromosome and then by feature size (in descending order):

    cat A.bed
    chr1 800 1000
    chr1 80  180
    chr1 1   10
    chr1 750 10000

    sortBed -i A.bed -sizeD
    chr1 750 10000
    chr1 800 1000
    chr1 80  180
    chr1 1   10

Disclaimer: it should be noted that `bedtools sort` is merely a convenience utility, as the UNIX sort utility will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file by chromosome then by start position in the following manner:

    sort -k 1,1 -k2,2n a.bed
    chr1 1   10
    chr1 80  180
    chr1 750 10000
    chr1 800 1000

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