Question: About beagle imputation
0
gravatar for r00628112
11 months ago by
r0062811210
r0062811210 wrote:

Hi~ everyone

I would like to impute the vcf file for further analysis.

I used the code as below:

java -jar beagle.25Nov19.28d.jar gt=191122-NKSC_newPmgenome.vcf out=Impt-191122-NKSC_newPmgenome.vcf impute=TRUE

The information showed:

Command line: java -Xmx27305m -jar beagle.25Nov19.28d.jar
  gt=191122-NKSC_newPmgenome.vcf
  out=Impt-191122-NKSC_newPmgenome.vcf
  impute=TRUE

No genetic map is specified: using 1 cM = 1 Mb
Exception in thread "main" java.lang.IllegalArgumentException: Duplicate marker: NC_024126.1    14964   .       C       .
        at vcf.Markers.markerSet(Markers.java:131)
        at vcf.Markers.<init>(Markers.java:85)
        at vcf.Markers.create(Markers.java:64)
        at vcf.BasicGT.markers(BasicGT.java:105)
        at vcf.BasicGT.<init>(BasicGT.java:86)
        at vcf.TargetData.targGT(TargetData.java:92)
        at vcf.TargetData.advanceWindowCm(TargetData.java:120)
        at vcf.TargetData.targetData(TargetData.java:77)
        at main.Main.data(Main.java:138)
        at main.Main.main(Main.java:110)

In the output file, I only got the log file

Could anyone give me some suggestions?

beagle imputation • 381 views
ADD COMMENTlink modified 11 months ago by ATpoint44k • written 11 months ago by r0062811210
1

These links might help:

beagle 4 exception: Duplicate marker Beagle imputation - duplication position error

ADD REPLYlink written 11 months ago by Fatima890
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