1. Community
2. General Discussion
3. GATK with Nanopore read

Hi Myo Naung, We don't have good information about GATK with Nanopore data. There is one conversation I found on our old forum site that may be helpful: https://sites.google.com/a/broadinstitute.or...

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• Genevieve Brandt (she/her)
• March 10, 2021 04:52
• 1 vote

1. Community
2. Germline
3. emit-ref-confidence error using single sample BAM

Hi suzy_bunters, yes we will get to this as soon as we are able. Please see our support policy. I think this problem has been addressed on the forum before, so I would recommend going through other...

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• Genevieve Brandt (she/her)
• March 09, 2021 19:05
• 1 vote

1. Community
2. Somatic
3. Interpretting CrosscheckFingerprints metrics

Hi Charlie, I am not sure what you mean by the software assuming a sample is a tumor or normal. Could you clarify your question? The LOD_SCORE_TUMOR_NORMAL is the log odds that the identity of two ...

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• Genevieve Brandt (she/her)
• March 02, 2021 19:06
• 1 vote

1. Community
2. Somatic
3. Interpretting CrosscheckFingerprints metrics

Hi Charlie Murphy, I am looking into the request again for better documentation, thank you for the feedback. I was able to find out more information about the LOD_SCORE_TUMOR_NORMAL vs the normal L...

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• Genevieve Brandt (she/her)
• February 26, 2021 18:09
• 1 vote

1. Community
2. Germline
3. Funcotator table format

Hi vctrymao, Please see the tool docs for Funcotator, MAF format is available but unsupported. So, you could try it anyway. I am not sure if it would work, but you could also check out the Variants...

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• Genevieve Brandt (she/her)
• February 17, 2021 18:08
• 1 vote

1. Community
2. Germline
3. How do I SelectVariants from GenomicsDB stored in GCS?

Lucas Taniguti just wanted to let you know we are still looking into this and will get back to you when we have updates.

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• Genevieve Brandt (she/her)
• February 12, 2021 17:29
• 1 vote

1. Community
2. Non-Human
3. Keras error in CNNScoreVariants

Hi jodybk, This is a known issue with CNNScoreVariants in GATK 4.1.9.0. You can read more about how to solve this here:  https://gatk.broadinstitute.org/hc/en-us/articles/360052489832-Known-Issue-w...

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• Genevieve Brandt (she/her)
• February 11, 2021 17:18
• 1 vote

1. Community
2. Non-Human
3. MarkDuplicatesSpark running, but not sorting/creating deduped bam files

Hi Vai Pathak, Spark opens a large number of temporary files while it runs and your issue is most likely from your system not allowing many files open at once. You can raise the limit for the allow...

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• Genevieve Brandt (she/her)
• February 10, 2021 23:02
• 1 vote

1. Community
2. Germline
3. GATK4 validateSam Errors interpretation

Hi mehar, We have a tutorial regarding interpreting these issues, have you seen this resource?  https://gatk.broadinstitute.org/hc/en-us/articles/360035891231-Errors-in-SAM-or-BAM-files-can-be-diag...

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• Genevieve Brandt (she/her)
• February 03, 2021 20:07
• 0 votes

1. Community
2. Other
3. Comparison between ReadsPipelineSpark and MarkDuplicates

Thanks for the update! That makes sense, glad we were able to figure out why you were seeing differences. I think that some of the issues in the documentation can be attributed to the BETA status o...

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• Genevieve Brandt (she/her)
• January 28, 2021 22:02
• 1 vote