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How to analyze separately called gVCFs?

I have VCFs from a WGS experiment on several thousand subjects.

I did not process the data through the GATK pipeline myself and have no access to the original BAM files or intermediary files.

Each individual BAM file was processed through GATK3 HaplotypeCaller to produce a gVCF using the emitRefConfidence=GVCF option. The resulting files were individually called using GenotypeGVCFs. I have these individually called VCFs and these are the only files I can access.

I understand that this is not recommended workflow, but I need to combine the resulting files and conduct an analysis on these results. (See https://gatkforums.broadinstitute.org/gatk/discussion/53/combining-variants-from-different-files-into-one) Any recommendations for combining these and proceeding?

Answers

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