The current GATK version is 3.6-0
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!

Register now for the upcoming GATK Best Practices workshop, Nov 7-8 at the Broad in Cambridge, MA. Open to all comers! More info and signup at https://goo.gl/forms/mFeERlIeLuJ95Idm1

GATK 2.7.4 -> PrintReads -> MESSAGE: Argument with name 'ds' isn't defined

Posts: 2Member

Hello,

I ran PrintReads with option -ds and got the error message showed in the title. Looking into docs, I see that there are other options for downsampling under CommandLineGATK like downsample to coverage, downsample to fraction, downsampling type. Am I right to think that the previous option -ds is equivalent to -dfrac combined with -dt ALL_READS?

Best regards,
Jacek

Tagged:

Hi @Jacek,

The downsampling arguments are -dt, -dcov and -dfrac. There is no combined version. Where did you see a downsampling argument named -ds? If you saw it in a doc somewhere please let me know and I will fix that mistake.

Geraldine Van der Auwera, PhD

• Posts: 2Member

Hmm, I saw that on the PrintReads documentation web page but, strangely, can't find it right now. I'll get back if I notice it again.

Could you please, however, explain how to use -dt. I thought it might be combined with either -dcov or -dfrac.

• United KingdomPosts: 400Member ✭✭✭

@Geraldine_VdAuwera --downsample_coverage / -ds also worked for me previously (2.4 or 2.5). I think @jacek might have seen it here: