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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.
Merging VCF files after HaplotypeCaller->VariantFiltration
I have a RNA dataset that I am calling variants (10 sample). After running gatk4 on all samples independently I want to merge the resulting VCF files for the downstream analysis that requires a multi sample VCF file. I tried to use vcf-merge and bcftools I realize that the INFO field of only one sample is included in the merged file.
How can I merge VCF files without loosing any information about samples ?