
Jacob Wang
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Activity overview
Latest activity by Jacob Wang-
Jacob Wang commented,
Hi, Anthony! Thank you for your quick response. I understand the support policy and I will wait for the updates.
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Jacob Wang created a post,
BQSR and VQSR resource for CHM13 (T2T) genome assembly
Hello! I am now mapping NGS data to the CHM13 (T2T) genome. I wonder how to perform BQSR and VQSR for I cannot find the resource of known sites for the CHM13 (T2T) genome. Does anyone know how to d...
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Jacob Wang commented,
Hi Yuxiang I read your post and I want to confirm with you on the following points. 1) You used "--use-jdk-deflater true --use-jdk-inflater true " in your GATK pipeline (BaseRecalibrator, Ap...
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Jacob Wang commented,
Hi, Genevieve Brandt (she/her) It's my pleasure to work with the GATK team and be able to contribute. I just ran the following steps (from merging gvcfs to annotation) using those gvcfs in the past...
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Jacob Wang commented,
Thanks, Pamela. I ran the following steps (from merging gvcfs to annotation) using the gvcfs in the past weekend. No problem happened. I think for now I can say the problem has been fixed. I will p...
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Jacob Wang commented,
Hi, Genevieve Brandt (she/her) I think I and Pamela Bretscher have solved the problem. I re-run both the steps of BQSR and HaplotypeCaller with the --use-jdk-inflater or --use-jdk-deflater option...
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Jacob Wang commented,
Hi, Pamela! Good news! I think we have solved the problem. I re-run for the two individuals both of the steps of BQSR and HaplotypeCaller with the --use-jdk-inflater or --use-jdk-deflater opti...
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Jacob Wang commented,
Hi Pamela Bretscher, I have run the two commands on my bam files as you suggested. I kept the intermediate bam files (after steps 3.Alignment, 4.Fixmate, 5.Sorting, 6.Deduplication and 9.BQSR) so I...
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Jacob Wang commented,
Hi Pamela, Thank you for the suggestion. I have run PrintBGZFBlockInformation for the .bam files (after the step of BQSR) of the three samples with the default parameters. The files generated b...
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Jacob Wang commented,
Hi Genevieve Brandt (she/her) Thank you all the same. I hope it could be solved in the future version.