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

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

jcajca Member Posts: 1

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

Best Answer

Answers

Sign In or Register to comment.