As reported here, a bug was found in VariantsToBinaryPED. Briefly, VariantsToBinaryPed expected the fam file to describe the samples in the same order as the input VCF file: if they were not in the same order, it did not correctly map sample IDs with the genotypes in the output binary PED.

We expect that in most use cases, the order would be the same (because PLINK uses lexicographic order, as does the GATK), so the bug would not impact results. However, as the user report demonstrates, in cases where order was different, the bug would seriously impact results.

We therefore recommend that anyone who has used VariantsToBinaryPED check their results for any inconsistencies in the kinship coefficients. Our apologies for the inconvenience to anyone who is affected by this bug, and big thanks again to user TimHughes for reporting the bug.

Finally, we have fixed the bug in GATK and released the fixed version under version number 2.7-4.

Comment on this article in the forum

At a glance

Follow us on Twitter

GATK Dev Team


Slides, tutorial materials from #GATK workshop in Leuven, Belgium posted at
19 Feb 17
RT @EMBL_ABR: Register your interest now in training in @gatk_dev @BroadGenomics to be run in Aus by @BioplatformsA…
19 Feb 17
#GATK Support team appreciation day -- say hi and get a prize!
23 Jan 17
RT @EricTopol: Great explainer of human genome structural variation @broadinstitute
21 Jan 17
@broadinstitute @TwinTwoG Sure, happy to help on the GATK forum; just post your question at
10 Jan 17

Our favorite tweets from others

@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
6 Jan 17
Really happy to have you again this year! @VIBLifeSciences
3 Jan 17
Currently in a time-out for saying that duck fat had a certain "je ne sais quack" at the thanksgiving dinner table.
25 Nov 16
@dgmacarthur @BioMickWatson @StevenNHart @splon There's even a shop near Broad that apparently fixes Hail code erro…
19 Nov 16
See more of our favorite tweets...
Search blog by tag

appistry ashg ashg16 benchmarks best-practices bug bug-fixed cancer cloud cluster cnv collaboration commandline community compute conferences cram cromwell denovo depthofcoverage diagnosetargets error forum gatk3 gatk4 genotype genotype-refinement genotypegvcfs google grch38 gvcf haploid haplotypecaller hg38 holiday hts htsjdk ibm intel java8 job job-offer jobs license meetings mendelianviolations mutect mutect2 ngs outreach pairhmm parallelism patch 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 syntax talks team terminology topstory troll tutorial unifiedgenotyper vcf-gz version-highlights versions vqsr wdl webinar workflow workshop xhmm