rand.md

rand

rand

Generate random genomic positions and ranges

Usage:
  rand [options] input

Arguments:
  input            Input FASTA, BAM, or VCF or BAM

Options:
  -n, --sites=SITES          Number of sites (default: 10)
  -b, --bed=BED              BED (0-based) of regions to restrict to
  -d, --dist=DIST            Output regions following a distribution ex: N(1,5) [see docs] (default: 0)
  -p, --pattern=PATTERN      A regular expression to use for chromosomes to keep
  -1, --one                  Output 1-based coordinates
  -h, --help                 Show this help

The rand command is useful for generating random sites and ranges. You can apply the rand command to fasta, bam, or vcf files.

If applied to a fasta file, the rand command will output the sequences.

Options

--pattern

Use --pattern to restrict chromosomes in output. For example, the human genome contains additional contigs for alternative haplotypes, or unplaced contigs (e.g. chrUn_gl000216). See this UCSC FAQ for more information.

sc rand --pattern "chr[0-9MXY]+$" hg19.fasta # only outputs chr1-22,X,Y,M

Examples

Sample regions with a normal distribution of \(N(\mu=5,\sigma=3)\).

sc rand --dist=5,3 hg19.fasta

Sample regions with a uniform distribution of \(U(min=2,max=10))

sc rand --dist=2-10 hg19.fasta

chr4	43446646	43446653	ATCTTTTA
chr2	146664347	146664354	aagattga
chr14	29047935	29047937	tca
...

Sample

0 vs. 1 based coordinates

rand automatically outputs coordinates that correspond to the input format. So:

• fasta - 0-based
• bam - 0-based
• vcf - 1-based

You can force fasta / bam output to be 1-based using the -1 flag.

Options

• n, --sites
• b, --bed
• -1 - Output 1-based coordinates instead of 0-based coordinates