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

Notice: Bug affecting ReduceReads -- GATK versions 2.0 and 2.1

Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,015 admin
edited September 2012 in Announcements

We have identified a major bug in ReduceReads -- GATK versions 2.0 and 2.1. The effect of the bug is that variant regions with more than 100 reads and fewer than 250 reads get downsampled to 0 reads.

This has now been fixed in the most recent release.

To check if you are using a buggy version, run the following:

    samtools view -H $BAM

This will produce the following output:

    @PG ID:GATK ReduceReads VN:XXX

If XXX is 2.0 or 2.1, any results obtained with your current version are suspect, and you will need to upgrade to the most recent version then rerun your processing.

Our most sincere apologies for the inconvenience.

Geraldine Van der Auwera, PhD

Tagged:
Sign In or Register to comment.