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.


Comment on this article in the forum



At a glance



Follow us on Twitter

GATK Dev Team

@gatk_dev

RT @WDL_dev: @BroadGenomics Storage pls. How does volume of bio material compare to volume of servers needed to store the data? https://t.…
29 Aug 16
RT @BroadGenomics: After the Samples Lab, we move into Extractions or Storage. What would you like to see next? #BroadGenomicsTour https://…
29 Aug 16
@BrandonDWomack Sure, just ask in the GATK support forum https://t.co/6z2bZ2AeN0
29 Aug 16
@thatdnaguy Note: future releases may switch to mem at some point. For our prod pipelines this is tied to shift to cloud.
26 Aug 16
@thatdnaguy @exac_exomes Same as first iirc, bwa aln as noted in supplemental doc https://t.co/ziwLjp7iIw
26 Aug 16

Our favorite tweets from others

it's the nightly build owl for GATK :D https://t.co/OwTRrk6KHA https://t.co/rfmAbdIIQp
11 Aug 16
We're going to make an hg38 version of ExAC. And we'll make @dgmacarthur pay for it. #BioinformaticsCampaignPromises
2 Aug 16
You’re right @gatk_dev honesty is key! About variants manual filtering: “In any case you're probably in for a world of pain.” Ha now I know!
11 Jul 16
.@gatk_dev I like the new documentation index page, the subheading has made my day! :D #doge #GeekHumourFTW https://t.co/9RXnDTMoBm
8 Jul 16
There is no NGS, NG is today so should only be called high-throughput sequencing #CSC #GATKworkshop https://t.co/paHcNimD7o
16 Jun 16
See more of our favorite tweets...
Search blog by tag

ad appistry ashg benchmarks best-practices bug bug-fixed cancer catvariants challenge cloud cluster commandline commandlinegatk community competition compute conferences cram cromwell denovo depthofcoverage diagnosetargets error fix forum gatk3 genotype genotype-refinement genotypegvcfs google grch38 gvcf haploid haplotypecaller hg38 holiday hts htsjdk ibm java8 job job-offer jobs joint-discovery license meetings mendelianviolations multisample multithreading mutect mutect2 ngs nt outreach pairhmm parallelism patch performance phone-home picard pipeline plans ploidy polyploid poster presentations printreads profile promote reference-model release release-notes rnaseq runtime saas script search selectvariants sequencing service slides snow speed status sting support syntax talks team terminology third-party-tools topstory trivia troll tutorial unifiedgenotyper variantannotator variantrecalibrator vcf-gz version-highlights versions vqsr wdl webinar workflow workshop