Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?