convert beagle genotypes to vcf
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8 weeks ago
bsp017 ▴ 40

Hi, I have a phased beagle file which I generated through Angsd v0.935. I would like to use the beagle utility program beagle2vcf.jar.

However I keep getting this error:

 java -jar beagle2vcf.jar rs markers bgl_comb ? > vcf
Exception in thread "main" java.lang.IllegalArgumentException: Alleles in Beagle and markers file are inconsistent for allele "0" and marker rs1
    at beagleutil.Beagle2Vcf.alleleCode(Beagle2Vcf.java:169)
    at beagleutil.Beagle2Vcf.main(Beagle2Vcf.java:69)

When I check the beagle and markers file the alleles look consistent. Here is the markers file:

rs1 A G
rs2 T C
rs3 A G

and the phased beagle file:

I id Ind0 Ind0 Ind1
M rs1 0 0 0
M rs2 3 3 3
M rs3 0 0 2
M rs4 1 1 1

Here is what the manual states:

usage: java -jar beagle2vcf.jar [chrom] [markers] [bgl] [missing] > [vcf]

where [chrom] = chromosome identifier in output VCF file.
[markers] = Beagle version 3 markers file. [bgl] = Beagle version 3 genotypes file. [missing] = missing allele code in Beagle genotypes file. [vcf] = output VCF file with a GT FORMAT field for each marker.

Markers in the markers file and Beagle genotypes file must be identical and sorted in order of increasing position. The first allele for a marker in the markers file will be the REF allele in the output VCF file. Alleles in the markers file must contain only 'A', 'C', 'G', and 'T' characters

Can anyone spot what is inconsistent in my files?

Thanks,

James

vcf beagle • 198 views
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