Jonathan Klonowski
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Recent activity by Jonathan Klonowski Sort by recent activity-
Yes, that is extremely useful and insightful. I guess my only followup question is: why does the GT tag even report phased genotypes if the "true" phasing information can be lost/jumbled, with the ...
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I thought I wrote out an answer and submitted but I dont see it :(((I was clarifying that for the example shown, I did not remove the `*` alleles from the g.vcf before the genotyping + phasing step...
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Ok, so you are suggesting that these symbolics might be necessary for phasing as they assist in the proper phasing of INDELs and SNPs that overlap, but after phasing they can be simply removed beca...
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Gökalp Çelik Ok, I just want to confirm that it is ok that, once youve split multiallelics to biallelics, it is ok to just `grep` or `SelectVariants` out any variants that have `*` as the alt allel...
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Is -A PossibleDeNovo no longer an option?
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No one actually looks at the comments. Lol. Useless.
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It is not clear by this article what the file extension is for the GenomicsDB object, where it is shored, how to find it, or how to identify it.
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can you append a gvcf to a previously created gendb database? for example: gatk GenomicsDBImport \ -V gendb://my_database -V data/gvcfs/mother.g.vcf \ -V data/gvcfs/father.g.vcf \ ...
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It is not clear at what step do you add the information from a new batch of genotyped samples to the previously genotyped information to solve the N + 1 problem. Do I run GenomicsDBImport on the ne...
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What purpose does --pedigree serve? It says "Pedigree file for determining the population "founders"", but I do not understand what the output is or what that output can be used for.