Question: Exception in thread "main" java.lang.IllegalArgumentException: Overlap between reference and non-reference samples
0
gravatar for valopes
7 months ago by
valopes30
valopes30 wrote:

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 • 782 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by valopes30

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

ADD REPLYlink written 7 months ago by Pierre Lindenbaum117k

I don't know how can I check it?

ADD REPLYlink written 7 months ago by valopes30
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
ADD REPLYlink written 7 months ago by Pierre Lindenbaum117k

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?

ADD REPLYlink written 7 months ago by valopes30

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.

ADD REPLYlink modified 7 months ago • written 7 months ago by Pierre Lindenbaum117k

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.

ADD REPLYlink written 7 months ago by WouterDeCoster36k
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