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Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

# 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.

• Posts: 112Member

@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