Jonathan Klonowski
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Activity overview
Latest activity by Jonathan Klonowski-
Jonathan Klonowski commented,
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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Jonathan Klonowski commented,
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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Jonathan Klonowski commented,
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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Jonathan Klonowski commented,
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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Jonathan Klonowski created a post,
Remove the `*` ALT Allele Reporting From a g.vcf Before (or After) Genotyping
I have a large scale dataset of WXS .g.vcfs , I do not have the original FASTA files. I would like to genotype these .g.vcfs into vcfs. These vcfs will be used in downstream applications. The issue...
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Jonathan Klonowski commented,
Is -A PossibleDeNovo no longer an option?
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Jonathan Klonowski commented,
No one actually looks at the comments. Lol. Useless.
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Jonathan Klonowski commented,
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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Jonathan Klonowski commented,
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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Jonathan Klonowski commented,
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...