```bash
docker run --rm quay.io/biocontainers/bedtools:2.31.1--h13024bc_3 bedtools shift -h
```

Tool:    bedtools shift (aka shiftBed)
Version: v2.31.1
Summary: Shift each feature by requested number of base pairs.

Usage:   bedtools shift [OPTIONS] -i <bed/gff/vcf> -g <genome> [-s <int> or (-p and -m)]

Options: 
	-s	Shift the BED/GFF/VCF entry -s base pairs.
		- (Integer) or (Float, e.g. 0.1) if used with -pct.

	-p	Shift features on the + strand by -p base pairs.
		- (Integer) or (Float, e.g. 0.1) if used with -pct.

	-m	Shift features on the - strand by -m base pairs.
		- (Integer) or (Float, e.g. 0.1) if used with -pct.

	-pct	Define -s, -m and -p as a fraction of the feature's length.
		E.g. if used on a 1000bp feature, -s 0.50, 
		will shift the feature 500 bp "upstream".  Default = false.

	-header	Print the header from the input file prior to results.

Notes: 
	(1)  Starts will be set to 0 if options would force it below 0.
	(2)  Ends will be set to the chromosome length if  requested slop would
	force it above the max chrom length.
	(3)  The genome file should tab delimited and structured as follows:

	<chromName><TAB><chromSize>

	For example, Human (hg19):
	chr1	249250621
	chr2	243199373
	...
	chr18_gl000207_random	4262

Tip 1. Use samtools faidx to create a genome file from a FASTA: 
	One can the samtools faidx command to index a FASTA file.
	The resulting .fai index is suitable as a genome file, 
	as bedtools will only look at the first two, relevant columns
	of the .fai file.

	For example:
	samtools faidx GRCh38.fa
	bedtools shift -i my.bed -g GRCh38.fa.fai

Tip 2. Use UCSC Table Browser to create a genome file: 
	One can use the UCSC Genome Browser's MySQL database to extract
	chromosome sizes. For example, H. sapiens:

	mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
	"select chrom, size from hg19.chromInfo"  > hg19.genome

