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3. GT values of VCF file generate by Mutect2

Some answers are explained like this: GATK assigns the genotype "0/1" for single nucleotide variants (SNVs) instead of "1/1".  Is it true?

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• Fiona Liang
• October 17, 2023 01:48
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2. General Discussion
3. What's the right order of Mitochondrial pipeline

Hi, Thank you. I'm still confused because the terra bucket on google clould is different form AlignAndCall.wdl. Steps in AlignAndCall.wdl are equal to those described in gatk mitochondrial best pra...

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• Fiona Liang
• August 15, 2023 08:43
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1. Community
2. General Discussion
3. What's the right order of Mitochondrial pipeline

Hi developer, Thank you for your reply. Where can I find files(or functions) called by AlignAndCall.wdl ? Program files in google cloud of terra are a little bit different from AlignAndCall.wdl. > ...

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• Fiona Liang
• August 14, 2023 08:24
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2. General Discussion
3. Mitochondrial LiftoverVcf

Thank you so much!

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• Fiona Liang
• August 12, 2023 06:19
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