1. Community
2. General Discussion
3. How can the difference between Mutect2 FORMAT fields FAD, F1R2, F2R2, SB and AD be explained?

Hi Eva König, Thank you for your question! AD and SB are a read based annotations while FAD, F1R2, and F1R2 are fragment based annotations. Fragment counting does not double count paired reads that...

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• Genevieve Brandt (she/her)
• April 04, 2022 21:19
• 1 vote

1. Community
2. Germline
3. Haplotypecaller 4.5.2.0 --alleles unexpected output

We were able to get a fix for this that will be in the next GATK release. https://github.com/broadinstitute/gatk/pull/7740 Thank you so much again for your very thorough files, they really helped u...

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• Genevieve Brandt (she/her)
• March 30, 2022 22:44
• 1 vote

1. Community
2. Somatic
3. Contig chr1_KQ031383v1_fix not present in the sequence dictionary

Hi zzh, This error indicates that the reference versions of your files do not match. There is a contig chr1_KQ031383v1_fix in one of your files that seems to be a non-standard contig name, so I wou...

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• Genevieve Brandt (she/her)
• March 29, 2022 20:12
• 1 vote

1. Community
2. General Discussion
3. Variants missing in 4.2.0.0 due to assembly cycles

I see! Could you please share the site as it is called in 4.1.8.1? And also a screenshot of the BAM and the bam output in IGV with the specific site highlighted (to see the depth)? What does this s...

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• Genevieve Brandt (she/her)
• March 16, 2022 19:02
• 1 vote

1. Community
2. General Discussion
3. Variants missing in 4.2.0.0 due to assembly cycles

Hi yqiu, I'm not sure what change specifically could be responsible for the differences you are seeing. All of our release notes are here: https://github.com/broadinstitute/gatk/releases, if you wa...

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• Genevieve Brandt (she/her)
• March 15, 2022 17:12
• 1 vote

1. Community
2. General Discussion
3. Target variants not in active region

Hi yqiu, It's generally pretty advanced to change the options that affect the active region determination, but there are a couple options you can try: --initial-tumor-lod --active-probability-thre...

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• Genevieve Brandt (she/her)
• March 15, 2022 17:04
• 1 vote

1. Community
2. Germline
3. GenomicsDBImport error from # fields in AS_UNIQ_ALT_READ_COUNT

Hi Jeff Gaither, This issue is coming from a bug with the AS_UNIQ_ALT_READ_COUNT. The annotation is not meant for germline use, so you won't need to have it in your file.  Here is another issue wit...

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• Genevieve Brandt (she/her)
• March 14, 2022 20:14
• 1 vote

1. Community
2. New User Advice
3. GATK MarkDuplicatesSpark output error

Hi Bilge Tabak, I don't see any sort of error in this program log. Could you run the program to completion and then post the error? Best, Genevieve

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• Genevieve Brandt (she/her)
• March 11, 2022 19:13
• 1 vote

1. Community
2. Documentation Questions
3. How to evlauate the result: GenotypeConcordance or Concordance

Yes, that's correct!

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• Genevieve Brandt (she/her)
• March 04, 2022 02:33
• 1 vote

1. Community
2. Documentation Questions
3. How to evlauate the result: GenotypeConcordance or Concordance

Yes! I can explain this.  In a multi-sample VCF, there is some information in the VCF that applies to all samples and some information that applies to each specific sample. The site level calculati...

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• Genevieve Brandt (she/her)
• March 02, 2022 19:45
• 1 vote