We have discovered a bug that seriously impacts the results of BQSR/ BaseRecalibrator when it is run with the scatter-gather functionality of Queue. To be clear, the bug does NOT affect BaseRecalibrator runs performed "normally", i.e. WITHOUT Queue's scatter-gather.

Consequences/ Solution:

Please be aware that if you have been using BaseRecalibrator scatter-gathered with Queue (GATK versions 2.0 and 2.1), your results may be wrong. You will need to redo the base recalibration of your data WITHOUT scatter-gathering.

This issue will be fixed in the next release (version 2.2). We apologize for any inconvenience this may cause you!


Comment on this article in the forum



At a glance



Follow us on Twitter

GATK Dev Team

@gatk_dev

RT @broadinstitute: .@NIH funds available for investigators in need of cloud computing & storage resources. Apply: https://t.co/IoiZMUNBM8
26 Apr 17
@DataKimist Enjoy! And let us know if we can help.
19 Apr 17
@mjpchaisson Not meant that way - just depending on what you're doing you may want to cite earlier framework or lat… https://t.co/QpIbwRf0bC
18 Apr 17
@cabioinformatic For more recent versions see https://t.co/QCbos5KBWw
15 Apr 17
@thatdnaguy @notigor @David_McGaughey @brent_p Indel Realign is redundant with assembly-based realign done by HC, w… https://t.co/77Lyil7BJY
13 Apr 17

Our favorite tweets from others

best error output: Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
4 Apr 17
From the @gatk_dev page describing .vcf files: "Don't write home-brewed VCF parsing scripts. It never ends well” https://t.co/28KcRoV14j
28 Feb 17
Our 3-day course on GATK https://t.co/mtN60KRTyS finished - 38 participants very happy! Big thanks to @gatk_dev team for excellent lessons.
24 Feb 17
@froggleston @dgmacarthur Sounds like ExAC is reaching Uber stage. ‘Uber but for pizza’. ‘ExAC but for wheat’.
14 Jan 17
#ESRenpeinture grad school - postdoc - after postdoc https://t.co/o3vQMgBDgk
6 Jan 17
See more of our favorite tweets...
Search blog by tag

appistry ashg ashg16 benchmarks best-practices bug bug-fixed cloud cluster cnv collaboration community compute conference conferences cram cromwell depthofcoverage diagnosetargets error forum gatk3 gatk4 genotype-refinement genotypegvcfs google grch38 gvcf haploid haplotypecaller help hg38 holiday hts htsjdk ibm intel java8 job job-offer jobs license meetings mutect mutect2 ngs outreach pairhmm parallelism patch pdf performance picard pipeline plans ploidy polyploid poster presentations printreads profile promote release release-notes rnaseq runtime saas script sequencing service slides snow speed status support talks team terminology topstory troll tutorial unifiedgenotyper vcf-gz version-highlights wdl workflow workshop xhmm