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Issues of Beagle version4.0
I am using Beagle4.0 to handle my vcf which generated through the GATK best practice workflow. However, I face a problem when using the Beagle ref resource: 1000G phase3 reference panel. It turns out to have no overlaps between my vcf and Beagle ref vcf, the result is the same with the conform-gt (a program for making alleles in a VCF file to be consistent with a reference VCF file).
Then, I run the GATK tools SelectVariants to test the concordance of my vcf and Beagle ref vcf, and the ERROR MESSAGE is : Input files chr4.1kg.phase3.v5.vcf and reference have incompatible contigs: No overlapping contigs found.
My GATK mapping reference is ucsc.hg19.fasta, not human_g1k_v37.fasta, does this has anything to do with the problem?