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

Hi Debora, I rolled back to GATK version 4.2.6.1 and that worked for me with the minimap2 reads. Allison

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• Allison Coomber
• February 20, 2023 22:15
• 1 vote

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

Hi Laura, Thank you so much! I used Minimap2 as well. I appreciate the help. Best, Allison

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• Allison Coomber
• February 09, 2023 22:43
• 1 vote

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

Hi, Did you ever solve this problem? I am having the same issue. I am trying to run HaplotypeCaller with two input BAMs, one from an Illumina sequencing experiment and one from an Oxford Nanopore r...

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• Allison Coomber
• February 09, 2023 16:35
• 0 votes