Beagle imputation error
0
0
Entering edit mode
7 weeks ago
PeterKW ▴ 40

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?

imputation Beagle • 153 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2675 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6