BAM to BED

Convert BAM file to BED file

Read Options

This tool has multiple read options to output.

• Read 1: output Read 1
• Read 2: output Read 2
• Combined: output combined reads
• Midpoint: output the midpoint between reads
• Fragment: output the full fragment of two reads

Note: The Midpoint and Fragment options requires proper mate-pair reading.

Command Line Interface

Usage:

java -jar ScriptManager.jar bam-format-converter bam-to-bed [-1 | -2 | -a | -m | -f]
[-hpsV] [-n=<MIN_INSERT>] [-o=<output>] [-x=<MAX_INSERT>] <bamFile>

Positional Input

This tool takes a single BAM file for input. As with other tools, this tool requires the BAM file be indexed.

Output Options

Option	Description
-o, --output=<output>	specify output directory (name will be same as original with .bed ext)
-s, --stdout	stream output file to STDOUT (cannot be used with -o flag)
-z, --gzip	gzip output (default=false)

Filter Options

These filter options are shared across all the BAM Format Converter tools.

Option	Description
-p, --mate-pair	require proper mate pair (default not required)
-n, --min-insert=<MIN_INSERT>	filter by min insert size in bp
-x, --max-insert=<MAX_INSERT>	filter by max insert size in bp

Read Options

Option	Description
-1, --read1	output read 1 (default)
-2, --read2	output read 2
-a, --all-reads	output combined
-m, --midpoint	output midpoint (require PE)
-f, --fragment	output fragment (requires PE)