Beagple 5.2 phasing error

0

Hi everyone,

I'm trying to phase a multi-sample (12 samples) vcf file with the first chromosome. I got this vcf after pruning with plink and recode it back to vcf. The file looks like this:

1 112 . C T . . PR GT ./. 0/1 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.
1 170 . T G . . PR GT 0/0 0/1 ./. 0/1 ./. 0/1 ./. 0/1 ./. 0/1 ./. ./.
1 370 . G A . . PR GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1 ./.
1 482 . T C . . PR GT ./. 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 0/1 ./. ./.
1 555 . C G . . PR GT ./. ./. ./. 0/1 ./. ./. ./. 0/1 0/1 ./. ./. ./.
1 1268 . G A . . PR GT ./. ./. ./. 0/1 0/0 0/1 ./. 0/1 ./. 0/1 ./. ./.
1 1946 . C G . . PR GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1 ./.
1 3014 . G T . . PR GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1 ./.
1 3392 . G A . . PR GT ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1 ./. ./.
1 3430 . C T . . PR GT ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1 0/1 ./.
1 3966 . G A . . PR GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1 ./.
1 3982 . C T . . PR GT ./. 0/0 ./. 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 ./.
1 4036 . A G . . PR GT ./. 0/1 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.

Now I'm trying to phase this file using beagle 5.2. My comand line looks like this;

java -jar /path-to-file/beagle.21Apr21.304.jar gt=file_pruned.vcf out=file_pruned_beagle_phased iterations=10

But I'm geting an error message that I think it has to do with MAF frequencies. But I don't really know what I'm doing wrong. Any suggestions are welcome!! 🙂

Exception in thread "main" java.lang.IllegalArgumentException: invalid array
at vcf.LowMafRefGTRec.throwArrayError(LowMafRefGTRec.java:149)
at vcf.LowMafRefGTRec.checkIndicesAndReturnMajorAllele(LowMafRefGTRec.java:143)
at vcf.LowMafRefDiallelicGTRec.<init>(LowMafRefDiallelicGTRec.java:129)
at vcf.RefGTRec.hapCodedInstance(RefGTRec.java:113)
at phase.Stage2Haps.recs(Stage2Haps.java:167)
at phase.Stage2Haps.lambda$stage2Haps$1(Stage2Haps.java:140)
at java.base/java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:271)
at java.base/java.util.stream.IntPipeline$1$1.accept(IntPipeline.java:180)
at java.base/java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:104)
at java.base/java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:699)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.Nodes$CollectorTask.doLeaf(Nodes.java:2191)
at java.base/java.util.stream.Nodes$CollectorTask.doLeaf(Nodes.java:2157)
at java.base/java.util.stream.AbstractTask.compute(AbstractTask.java:327)
at java.base/java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:746)
at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290)
at java.base/java.util.concurrent.ForkJoinTask.doInvoke(ForkJoinTask.java:408)
at java.base/java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:736)
at java.base/java.util.stream.Nodes.collect(Nodes.java:336)
at java.base/java.util.stream.ReferencePipeline.evaluateToNode(ReferencePipeline.java:109)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:545)
at java.base/java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
at java.base/java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:517)
at phase.Stage2Haps.stage2Haps(Stage2Haps.java:141)
at phase.PhaseLS.runStage2(PhaseLS.java:269)
at main.Main.phaseStage2Variants(Main.java:209)
at main.Main.phaseTarg(Main.java:182)
at main.Main.phaseAndImpute(Main.java:171)
at main.Main.main(Main.java:126)

Thanks,

Pedro


vcf


beagle


plink


phasing

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