Beagle imputation error

Question

[PKW]

Hi,

I am using Beagle to impute missing genotype calls but I get the error below:

Exception in thread "main" java.lang.IllegalArgumentException: 0 at vcf.Samples.checkForDuplicates(Samples.java:70) at vcf.Samples.<init>(Samples.java:58) at vcf.Samples.combine(Samples.java:100) at vcf.XRefGT.combine(XRefGT.java:72) at phase.CodedSteps.<init>(CodedSteps.java:59) at phase.PhaseData.codedSteps(PhaseData.java:200) at phase.PhaseLS.pbwtPhaseIbs(PhaseLS.java:86) at phase.PhaseLS.runStage1(PhaseLS.java:57) at main.Main.phaseStage1Variants(Main.java:193) at main.Main.phaseTarg(Main.java:181) at main.Main.phaseAndImpute(Main.java:171) at main.Main.main(Main.java:126)

This is the code that I am running:

java -Xmx100000m -jar beagle.28Jun21.220.jar burnin=12 iterations=20 phase-states=3200 imp-states=3200 ne=1000 nthreads=30 window=400 ref=ref_vcf.vcf.gz gt=target.vcf.gz out=beagle_target.vcf

I can't figure out what the problem is, any help?

[PKW]

I got the problem, some samples were appearing in the reference and target sets. Sorry guys, I should have tested this before posting the question.

Answer 1

[Jiong]

I also met this problem, could any one gives a solution? thanks

[PKW]

Hi Jiong, check that you don't have the same samples appear in both the reference and target set.