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Merging GVCF or VCF? #296

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alanlamsiu opened this issue Nov 1, 2023 · 0 comments
Open

Merging GVCF or VCF? #296

alanlamsiu opened this issue Nov 1, 2023 · 0 comments

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@alanlamsiu
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I have dozens of GVCF files generated by DeepVariant from WGS data to be merged but I don't seem to have enough memory for GLnexus to complete the job. Is it the only solution to bin the entire genome properly and split the job into different genomic bins?

On the other hand, if I used VCF files instead of GVCF files, GLnexus was done succcessfully. Is this a proper way to merge the genotypes from different samples?
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@alanlamsiu