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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 ?