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!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

#### ☞ Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ` ) each to make a code block as demonstrated here.

GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Member Posts: 36
edited September 2012

Hallo everyone,
I have a question about ReduceReads when using scatter/gather. In the argument details of ReduceReads you write for the parameter -nocmp_names:
"... If you scatter/gather there is no guarantee that read name uniqueness will be maintained -- in this case we recommend not compressing."

Do you mean, that if I use scatter/gather, I should use ReduceReads with the -nocmp_names option so that the read names will not be compressed
OR
do you mean that I should not use ReduceReads at all when scatter/gathering.

I assume the first is meant, I just wanted to make sure. Thank you for your time and effort.
Eva

Post edited by Geraldine_VdAuwera on

Yes, don't compress read names when running ReduceReads scatter/gathered across chromosomes, of you'll end up with many reads with the same read name (bad for the SAM spec).

--
Mark A. DePristo, Ph.D.
Co-Director, Medical and Population Genetics
Broad Institute of MIT and Harvard