SelectVariants -number, and missing images from docs....

jca

Hello,

I've a couple of essentially documentation-centric questions...

Firstly, the SelectVariants documentation describes selecting 1000 random variants from a vcf using '-number 1000', however when I try that (with the command "java -jar GenomeAnalysisTK.jar -T SelectVariants -R human_g1k_v37.fasta --variant variants.vcf -o 1000.vcf -number 1000") it produces the error 'Argument with the name number isn't defined'. Trying --number instead doesn't make any difference, while the --help output does not list this argument (GATK 2.2.2). It this option no longer available?

Secondly, the 'gatkforums.broadinstitute.org/discussion/48/using-varianteval#Understanding_Genotype_Concordance_values_from_Variant_Eval' section of the 'Using VariantEval' page has a series of images explaining the concordance values, however the images are missing. Please could these be restored?

Many thanks, James

Geraldine_VdAuwera

Hi James,

The -number argument has indeed been removed. We'll update the docs to reflect that. And yes, we'll restore the images very soon, sorry about that.

jca

Thanks Geraldine. I was beginning to think I was incapable of typing 'number' correctly!

Geraldine_VdAuwera

Ah, I feel your pain.

The tech docs have been updated and the change will be visible with the next subrelease. In the meantime, images have been restored in the "Using VariantEval" document.

http://gatkforums.broadinstitute.org/discussion/48/using-varianteval