GATK pileup with merged BAM files
 

I have several lanes of sequences which I have merged into one BAM file. I then processed this merged BAM file through GATK: recal, dedup, etc. I want create a pileup from the merged BAM file using GenomeAnalysisTK.jar -T Pileup . Is there a way to perform this pileup with the lanes separated? When I run Pileup on the merged BAM file, output exists, but it is unclear from which lane the output is generated.