GATK base quality recalibration suppose to keep old and new quality scores?

[Heisman]

Hey guys,

Simple question. After performing base quality recalibration , if I convert the bam files to sam it's obvious that new quality scores appear where old ones were but the old quality scores are still retained in a later field. Is it possible to delete these older values? I'm not sure if they would affect downstream analysis in any way but if nothing else they make the bam file a lot larger than it needs to be.

[Heisman]

Does anybody have an answer for this? Does everybody else see the same thing (that aligned files grow because old and new quality scores are replaced)? Would it be appropriate to manually delete the older base quality scores?

[maubp]

I don't know what uses the "old" scores, but you certainly could write a script to remove them.