sam2bed {Rsubread} | R Documentation

## Convert a SAM format file to a BED format file

### Description

SAM to BED conversion

### Usage

    sam2bed(samfile,bedfile,readlen)

### Arguments

`samfile` | character string giving the name of input file. Input format should be in SAM format.
`bedfile` | character string giving the name of output file. Output file is in BED format.
`readlen` | numeric value giving the length of reads included in the input file.

### Details

This function converts a SAM format file to a BED format file, which can then be displayed in a genome browser like UCSC genome browser, IGB, IGV.

### Value

No value is produced but a BED format file is written to the current working directory. This file contains six columns including chromosomal name, start position, end position, name(‘.’), mapping quality score and strandness.

### Author(s)

Wei Shi

[Package Rsubread version 1.34.7 Index]