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Brief summary: When running non-human whole genome sequencing sample following somatic CNV pipeline (How to part II) Sensitively detect copy ratio alterations and allelic segments – GATK (broadinst...

• Yuwei Bao
• June 25, 2024 21:39
• Edited
• 2 followers
• 5 comments
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1. Community
2. Non-Human

REQUIRED for all errors and issues: a) GATK version used: docker image spacecade7/tutorial_11682_11683:gatk4.0.1.1 b) Exact command used: docker run -v WORKDIR/./:WORKDIR/./ spacecade7/tutorial_1...

• Yuwei Bao
• June 23, 2024 21:07
• Edited
• 2 followers
• 2 comments
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1. Community
2. Somatic

REQUIRED for all errors and issues: a) GATK version used: docker image spacecade7/tutorial_11682_11683:gatk4.0.1.1b) Exact command used: tutorial1=./gatk_CNV/tutorial/tutorial_11682tutorial2=./ga...

• Yuwei Bao
• June 21, 2024 19:35
• Edited
• 2 followers
• 3 comments
• 0 votes

1. Community
2. Somatic

REQUIRED for all errors and issues: a) GATK version used: docker image: tutorial_11682_11683:gatk4.0.1.1 b) Exact command used:  gatk --java-options "-Xmx3g" CollectAllelicCounts    \       -I s...

• Yuwei Bao
• March 02, 2023 20:45
• 2 followers
• 1 comment
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1. Community
2. Somatic

Hi everyone: I am using GATK v4.2.6.1 and I have trouble producing Panel of Normal for somatic mutation calling using the following workflow from the tutorial :   Step 1: Run Mutect2 in tumor-only ...

• Yuwei Bao
• October 12, 2022 00:51
• 2 followers
• 2 comments
• 0 votes