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3. Variant not called by HaplotypeCaller (not called in father, but present in child)

Hi James, I tested 4.5.0.0 once again as you suggested. When running with `--alleles` using the VCF from the child, the variant is revealed: 21  34923904    .   C   T   1457.64 .   AC=1;AF=0.500;AN...

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• Rolf Schröder
• February 06, 2024 06:30
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1. Community
2. Germline
3. Variant not called by HaplotypeCaller (not called in father, but present in child)

Hey James, thank you very much for that answer. In the meantime, I had also looked for repetitive sequences and realized that this might be the culprint. Here are my results for now. I will test yo...

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• Rolf Schröder
• February 06, 2024 06:11
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1. Community
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3. Haplotype calls deletion followed by insertion instead of indel

Hey Louis, thanks a lot. This does help a lot for my understanding!

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• Rolf Schröder
• April 25, 2023 06:34
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