ATLAS / Sequence Data Processing Tools: mergeRG

Input

• A BAM file

• A .txt file, e.g. mergeTheseRGs.txt :

A file that specifies on each line the name of the new, combined read group and all the read groups that shall be renamed as the common read group (tab separated)

Output

A new bam file with suffix _mergedRGs.bam

Usage Example

./atlas task=mergeRG bam=example.bam readGroups=mergeTheseRGs.txt


Specific Commands

• readGroups : Specify a .txt file, which on each line contains the name of the new read group and the names of the read groups that shall be merged in order to form this new read group.

Engine Parameters

Engine parameters that are common to all tasks can be found here.

Updated