sam2bed {Rsubread} | R Documentation

## Convert a SAM Format File to a BED File

### Description

This function performs SAM to BED conversion. Each read in the SAM input is converted into an interval in the BED file.

### Usage

    sam2bed(

        samfile,
        bedfile,
        readlen)

### Arguments

`samfile` | a character string giving the name of input file. Input format should be in SAM format.
`bedfile` | a character string giving the name of output file. Output file is in BED format.
`readlen` | a 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. This function does not find the read length from the SAM file, but requires the user to specify the read length.

### 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 2.4.3 Index]