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gVCFs for Targeted Resequenced data


For targeted re-sequenced data, can we do variant calling using HaplotypeCaller in gVCF mode followed by using GenotypeGVCFs for joint genotyping ?

Would the following best practices work for targeted re-sequencing as well , except for VQSR as for targted resequencing GATK advices another way of filtering.


Best Answer


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