## Bug Bulletin: AD swapping by SelectVariants with -nt in 2.x versions

### Posted by Geraldine_VdAuwera on 11 Apr 2014 (1)

This is not exactly new (it was fixed in GATK 3.0) but it's come to our attention that many people are unaware of this bug, so we want to spread the word since it might have some important impacts on people's results.

Affected versions: 2.x versions up to 2.8 (not sure when it started)

Affected tool: SelectVariants

Trigger conditions: Extracting a subset of samples with SelectVariants while using multi-threading (-nt)

Effects: Genotype-level fields (such as AD) swapped among samples

This bug no longer affects any tools in versions 3.0 and above, but callsets generated with earlier versions may need to be checked for consistency of genotype-level annotations. Our sincere apologies if you have been affected by this bug, and our thanks to the users who reported experiencing this issue.

#### ArthurGoldberg

Also SelectVariants reordered PL values in genotypes of variants with multiple alternate alleles.

#### GATK Dev Team

###### @gatk_dev

@BrianPardy Great, thanks for the feedback!
###### 28 Sep 16
@BrianPardy Thank you! Does anything in particular stand out? We'd love to know what people find most useful so we can do more of the same.
###### 28 Sep 16
#GATK workshop crew is in Basel, ready to roll! @ISBSIB https://t.co/m56JzpC1bN
###### 25 Sep 16
@thatdnaguy That's right, we've retired it, see https://t.co/epbvwOQVTt
###### 23 Sep 16
@geoffjentry @BroadGenomics Ah, you should ask @WDL_dev on the WDL forum then :)

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