Hi, I am trying to impute missing SNPs using beagle4. However, I am getting the error message, Could you help please?
No genetic map is specified: using 1 cM = 1 Mb
Exception in thread "main" java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: ERROR: missing REF or ALT allele at 5:35101444
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:593)
at java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:677)
at java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:735)
at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:714)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at vcf.VcfIt.fillEmissionBuffer(VcfIt.java:307)
at vcf.VcfIt.next(VcfIt.java:363)
at vcf.VcfIt.next(VcfIt.java:52)
at vcf.IntervalVcfIt.readFirstRecord(IntervalVcfIt.java:99)
at vcf.IntervalVcfIt.<init>(IntervalVcfIt.java:59)
at main.Main.nonRefData(Main.java:261)
at main.Main.main(Main.java:111)
Caused by: java.lang.IllegalArgumentException: ERROR: missing REF or ALT allele at 5:35101444
at vcf.BasicMarker.checkAlleles(BasicMarker.java:130)
at vcf.BasicMarker.extractAlleles(BasicMarker.java:312)
at vcf.BasicMarker.<init>(BasicMarker.java:249)
at vcf.VcfRecGTParser.<init>(VcfRecGTParser.java:70)
at vcf.BitSetGT.<init>(BitSetGT.java:74)
at vcf.VcfIt.lambda$static$6(VcfIt.java:90)
at vcf.VcfIt.lambda$new$7(VcfIt.java:192)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:747)
at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:721)
at java.util.stream.AbstractTask.compute(AbstractTask.java:316)
at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
•
written
by
ericagoyi •
Beagle 4 has an issue if the ALT allele is not defined and instead if it is just represented by a "." when genotype is 0/0.
Workaround is to use Beagle 3 or exclude rows with MAF=0.
Here is the best solution:
bcftools view -i 'ALT !="-" | REF!="-"' All_samples_Exome.vcf.gz -Ov -o All_samples_Exome_clean.vcf
details:
Hi,
How does this line do any sort of imputation? It only subsets a VCF file, which is not what OP asked for 3.2 years ago.
Given that your answer doesn't address OP's problem in the first place, how can it be the "best" solution?
Please invest a little more thought in your answers.
Log in to answer this question.
Did you check the locus it mentions ( 5:35101444 ) to see if there's anything wrong in the data?
Please use the formatting bar (especially the
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.