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

Question

[valopes]

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!

[Pierre Lindenbaum]

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

[valopes]

I don't know how can I check it?

[Pierre Lindenbaum]

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

[valopes]

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?

[Pierre Lindenbaum]

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.

[WouterDeCoster]

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.