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2. Germline
3. Unable to trim uncertain bases without flow order information

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
• February 15, 2023 08:53
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1. Community
2. New User Advice
3. Using GATK as a genotyper to genotype existing variants

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
• October 25, 2021 17:07
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1. Community
2. New User Advice
3. Using GATK as a genotyper to genotype existing variants

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
• October 13, 2021 09:02
• 0 votes