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VariantFiltration: vcf and reference have incompatible contigs
Hi, I got an error during VariantFiltration step stating " GATK_All_Variants.vcf and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information." i cheked the link and it suggested to remap using the right reference. However I have used the same reference for mapping that I am providing for variantFiltration. Along the way I have just used the training set for base recalibration before calling the variant. Can you suggest something?