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Exception in thread "main" java.lang.IllegalArgumentException: Overlap between reference and non-reference samples

Hi all,

Did someone already face this problem working with Beagle 4?

I am running:

java -Xmx25000m -jar beagle.jar ref=ref-panel.vcf.gz gt=input.vcf out=output.vcf

and I am getting:

No genetic map is specified: using 1 cM = 1 Mb

Exception in thread "main" java.lang.IllegalArgumentException: Overlap between reference and non-reference samples: xxx

at vcf.AllData.checkSampleOverlap(AllData.java:133)

at vcf.AllData.<init>(AllData.java:83)

at vcf.AllData.allData(AllData.java:79)

at main.Main.allData(Main.java:329)

at main.Main.main(Main.java:111)

I have no idea on what to do.

Could someone please help me?

Thanks a lot!

snp
• 4,313 views • link
written by valopes • valopes

check each vcf files: do you have two SNPs at the very same positions ?

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

I don't know how can I check it?

• 1 views • link
written by valopes • valopes 
gunzip -c ref-panel.vcf.gz| grep -v "#" | cut -f 1,2 | sort | uniq -d

cat output.vcf | grep -v "#" | cut -f 1,2 | sort | uniq -d
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

I did

gunzip -c ref-panel.vcf.gz| grep -v "#" | cut -f 1,2 | sort | uniq -d > ref-panel-test.vcf

cat ref-panel-test.vcf | grep -v "#" | cut -f 1,2 | sort | uniq -d > ref-panel-test2.vcf

It didn't work! What am I doing wrong?

• 0 views • link
written by valopes • valopes

It didn't work!

of course

the input won't be a vcf file but a set list duplicated positions. If any outputs are not empty then it means that you have some duplicated REF/POS. And again, I'm not sure it's the primary cause of the error.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

It didn't work!

That's not very informative. You should explain what happened and which error you obtained, or how the output is not what you expected.

• 0 views • link
written by WouterDeCoster WouterDeCoster

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