The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

Discard original quality scores after recalibration in GATK v2

cbuxtoncbuxton Member Posts: 2

In GATK 1.x there was an option to discard the original quality scores for a recalibrated bam using the switch:
--doNotWriteOriginalQuals
I think during TableRecalibration

Is there an equivalent in GATK v 2.x since as far as I can see t here is no option in PrintReads after BaseRecalibrator to discard original quality scores in favour of recalibrated quality scores.
My intention is to keep the file sizes down as much as possible
Thanks

Best Answer

Answers

Sign In or Register to comment.