The current GATK version is 3.4-46

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 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:

Answers

• Posts: 8,688Administrator, GATK Dev admin

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: 393Member ✭✭✭

@Geraldine_VdAuwera --downsample_coverage / -ds also worked for me previously (2.4 or 2.5). I think @jacek might have seen it here:
http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html

In case anyone else comes across this thread, then dfrac is mentioned on the CommandLineGATK documentation page:
http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_CommandLineGATK.html

• Posts: 8,688Administrator, GATK Dev admin

Ah yes, PrintReads does have its own downsampling argument. It's a fossil of the early days of GATK which we need to clean out at some point to avoid confusion. Thanks for pointing it out, @tommycarstensen !

Geraldine Van der Auwera, PhD

Sign In or Register to comment.