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3. Target variants not in active region

Thanks for the quick response and suggestions! I tried them separately.  Unfortunately, neither parameter can rescue the variants. I tried --initial-tumor-lod 1 and --active-probability-threshold d...

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• yqiu
• March 19, 2022 05:43
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3. Mutect2 AF does not match AD and DP

Hi Genevieve, Thanks for the response and the link you shared is very useful. But it may not directly relate to my question. I get that there are some reads are uninformative and they are not count...

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• yqiu
• March 18, 2022 16:42
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3. Target variants not in active region

Hi Genevieve, Thanks for the detailed response! Do you have any suggestions about which parameter to adjust and suggested values? Or should I adjust both of them? For --initial-tumor-lod, should I ...

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• yqiu
• March 18, 2022 00:50
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3. Variants missing in 4.2.0.0 due to assembly cycles

Hi Genevieve, Thanks for the response! Please see the answers to your questions below. Here is the SNV as called in GATK 4.1.8.1. CHROM    POS    .    C    T    .    .    AS_SB_TABLE=9605,9821|113...

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• yqiu
• March 17, 2022 23:50
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3. Variants missing in 4.2.0.0 due to assembly cycles

Thanks a lot for the suggestion! Following your previous advise, we did use --max-reads-per-alignment-start to 0 in both GATK 4.1.8 and GATK 4.2 in the results I mentioned above. 

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• yqiu
• March 15, 2022 18:30
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3. Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start

Hi Genevieve, Sorry for the delay in response. Thanks for the suggestion. We have no problems when disable subsampling as you suggested. Best, Yunjiang

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• yqiu
• March 07, 2022 22:59
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3. Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start

Hi Genevieve, Thanks a lot for the prompt reply.  Could you help explain a little bit more about why "Not necessarily 4000 would be a subset of 12000"? There might be something about downsampling t...

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• yqiu
• January 13, 2022 04:50
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3. Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start

Hi Genevieve, Thanks a lot for the suggestion and explanation with downsampling. We will disable downsampling for amplicon data.  But it still unclear to me why there are reads with --max-reads-per...

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• yqiu
• January 12, 2022 22:35
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3. Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start

Thanks a lot for the suggestion! We will disable downsampling for now as you suggested. But it would be great to learn about the reason underlying downsampling though we do understand it is non-tri...

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• yqiu
• January 12, 2022 17:55
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3. Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start

Sorry for the confusion. Yes. All the data we showed are amplicon data without UMIs.

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• yqiu
• January 11, 2022 21:48
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