
Genevieve Brandt (she/her)
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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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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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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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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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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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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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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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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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Yes, that's correct!
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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...