1. Community
2. New User Advice
3. Steps For GATK-gCNV pipleline on Exome Data

Yes, this file must be in TSV format. I was speaking very generally about Bayesian inference https://en.wikipedia.org/wiki/Bayesian_inference. If your inferences depend very sensitively on the part...

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• Samuel Lee
• April 03, 2023 22:05
• Edited
• 1 vote

1. Community
2. Germline
3. Can't generate ploidy-calls directory and ploidy-calls/SAMPLE_0 when use DetermineGermlineContigPloidy

Hi Chipmunks, can you double check the formatting of your contig-ploidy priors table file? For instance, please ensure that it is tab separated. The first column header should also be `CONTIG_NAME`...

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• Samuel Lee
• March 20, 2023 18:31
• 1 vote

1. Community
2. Germline
3. GermlineCNVCaller in CASE mode using too many CPU for denoising

Hi Xscrapert, can you try adjusting the `OMP_NUM_THREADS` and `MKL_NUM_THREADS` environment variables? E.g., `export OMP_NUM_THREADS=4`. Apologies---these are set in the official WDLs, but I see no...

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• Samuel Lee
• February 27, 2023 18:26
• 1 vote

1. Community
2. Documentation Questions
3. CallCopyRatioSegments -- how does it work?

Yes, that's correct that the z-score thresholds do not come into play. You might want to adjust the parameters to be more sensitive. If I recall, these default parameters were tuned for a clinical ...

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• Samuel Lee
• February 15, 2023 02:44
• Edited
• 1 vote

1. Community
2. Documentation Questions
3. CallCopyRatioSegments -- how does it work?

Hi Austin Southard-Smith, Apologies for the confusing behavior and scant (or missing, in the case of ReCapSeg) documentation. I think the bit of code at https://github.com/broadinstitute/gatk/blob/...

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• Samuel Lee
• February 13, 2023 19:25
• Edited
• 1 vote

1. Community
2. General Discussion
3. GATK CNV caller cohort mode long running

Hi Anjali Kumari, Can you provide more information about the input intervals given by hg38.interval_list? If I understand correctly, your 67M interval_list.tsv output corresponds to these input int...

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• Samuel Lee
• July 11, 2022 20:41
• Edited
• 1 vote

1. Community
2. Somatic
3. Generating ACS like output from new GATK CNV pipeline (WGS)

Hi Jett Crowdis, Thanks for your question. I've tried to answer it here: https://github.com/broadinstitute/gatk/issues/6685

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• Samuel Lee
• July 01, 2020 13:19
• 1 vote

1. Community
2. Other
3. Broken: conda env create -n gatk -f gatkcondaenv.yml

Himawari, if you create a file gatkcondaenv.yml that contains the block of text in https://gatk.broadinstitute.org/hc/en-us/community/posts/360061666671/comments/360010377231, you should be able to...

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• Samuel Lee
• May 15, 2020 14:50
• 1 vote

1. Community
2. Other
3. Broken: conda env create -n gatk -f gatkcondaenv.yml

Hi James White and Carlos Luna, Can you test the new YML file from the PR that Bhanu Gandham references above (https://github.com/broadinstitute/gatk/pull/5026#issuecomment-621371506)?  I reproduce...

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• Samuel Lee
• May 12, 2020 16:58
• Edited
• 1 vote

1. Community
2. Somatic
3. Sample intervals must be identical to the original intervals used to build the panel of normals

When constructing the panel, you pass `-L intervals_list_hg19.bed` to CollectReadCounts.  However, for the case sample, you instead pass `-L targets_C.preprocessed.interval_list` to CollectReadCoun...

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• Samuel Lee
• March 02, 2020 14:21
• 1 vote