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*The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.
*The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.
*The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.
*The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.
*One potential concern of this pipeline is file size, since each sample now has its own VCFs (~2Gb for chr20 per sample).
*One potential concern of this pipeline is the number and size of additional files, since each sample now has its own set of VCFs (~2Gb for chr20 per sample).
==Contact==
==Contact==
Please contact Yancy if you have any questions.
Please contact Yancy if you have any questions.
