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.

Fri 11 Apr 2014




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@geoffjentry @PatriciaMBrent Indel realn gone now; much faster BQSR + Sparkified tools in GATK4a. And wider scope of application/ use cases.
9 Dec 16
@geoffjentry @PatriciaMBrent B fair, other slide says results similar. Not uncommon for benchmark tests. But speed comparison v outdated 1/2
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RT @geoffjentry: Talk by Stavros Papadopoulos about TileDB from @intel - used by @BroadGenomics to power our joint genotyping https://t.co/
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@iskander @NJL_NGS Hm. Can you please post this in the forum?
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@iskander @NJL_NGS Treat them like any other read, no special handling. Problems arise in CIGAR functions that don’t know how to handle Ns.
7 Dec 16

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