Hanbing Song
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Recent activity by Hanbing Song
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Hi Samantha, Thanks for your reply! I found that .bed file also worked when inserted as the interval. However, I kept hitting the same error during the denoisedcount step. Strangely, when I downlo...
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Hi Samantha, Thanks for pointing it out! But I only have a .bed file for our target kit. Is there a way of converting it to the interval_list format or .bed file also works? In the meantime, in t...
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Hi Samantha, Thanks for following up on this issue and thanks for reaching out to GATKdevelopers for help! Got it, I'll change the gatk version and test it out again soon. We just figured out w...
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Hi Samantha, Thanks so much for spotting this. However, I still ran into this error in this step PlotDenoisedCopyRatiosNormal. The problem is that I have 24 samples in this batch and 11 seemed t...
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Yes, sure! Sorry bout not including that. The job ID is a2756ae7-b331-4ea3-8c0b-0843a18aea88.
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Hi Samantha, I restarted the workflow this morning and so far some of the samples failed again on the plotdenoised step and the funcotator step. I changed the funcotator datasource and didn't see ...
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Hi Samantha, Sure! I'll just reply to this thread then. Yeah, that makes a lot of sense. Thank you for the insight! I just modified the funcotator datasource to the 1.6.20190124 version and resta...
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Hi Samantha, Yes, that was the same problem because I don't know which forum would be the proper one to post this. The submission ID would be this one: 7878b8f7-2f4e-4c9e-9492-1052b0ce5c00. Th...
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Hi Samantha, Thanks for your reply and I just shared our workspace with you. The workspace name is fhuanglab/WES_pipeline. In there you might see the latest failed job running 2-CNV_Somatic_Pair...
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Hi Jason, Thanks for following up on this. I talked to Dr. Josh Gould who made the dropseq_workflow and he helped me figure out the problem. The input sample list should be comma-delimited. But in...
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