Ivar Grytten
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Latest activity by Ivar Grytten-
Ivar Grytten commented,
I had the same issue with Minimap2. It seems that it is the TP:A:P field that Minimap2 outputs that is causing trouble. For some reason, it triggers hardclipping in GATK, which then fails for some ...
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Ivar Grytten commented,
Thanks a lot for clarifying! It does indeed make sense that GATK does suggest (call) alleles that it finds support for on the given sites. I just assumed that GATK with --alleles dit not behave thi...
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Ivar Grytten commented,
Thanks for the reply! I would expect GATK to genotype the G/T SNP as either 0/0, 0/1 or 1/1, not to suggest another SNP G/A that is not in the input vcf. As another example, if I ask GATK to genoty...
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Ivar Grytten created a post,
Using GATK as a genotyper to genotype existing variants
AnsweredHi!I want to use GATK only as a genotyper to genotype a set of input variants (e.g. variants from 1000 Genomes). From what I have understood from the documentation (and other papers that benchmark ...