picard.jar SamToFastq "paired reads have different names"

Question

[sami.hailu.15]

Hi,

I'm trying to convert a bam file into paired fastq files using picard:

picard.jar SamToFastq input.bam F=one.fq F2=two.fq NON_PF=true

But the oputput files one.fq and two.fq seem to have different names for paired reads. Can someone suggest me other ways of generating paired reads with same name?

Thanks Sami

[GenoMax]

See @Brian's answer here for an alternate option: How to extract all the mapped reads from bwa output