bkelly · ✭
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Does haplotypecaller still have internal downsampling that we, as users, can't turn off? I have seem similar behavior which I assumed was due to downsampling. The downsampling seems random based on the start of your interval region. It would be r…
Can you explain the version numbering scheme? Does 3.4-46 include the bug fixes promised for 3.4-1? It seems like it went from 3.4 to 3.4-46 with nothing in between (I'll admit I don't check the download page daily). Are there any patch release n…
Thank you @Sheila. Please let me know if there is any more data/info I can provide that would be of help.
Was there any resolution to this bug? I'm seeing a similar result in a similar situation, but it seems to be dependant on whether I merge GVCFs before genotyping or just genotyping all the samples from seperate GVCFs. What I'm most interested is t…
Thanks for the reply. It does appear that I copied the wrong lines, but I double checked these. The first is from ts_filter_level=90: ##FILTER=<ID=TruthSensitivityTranche90.00to99.00,Description="Truth sensitivity tranche level at VSQ Lod…