Andrew Carroll

Hi @pgrosu Thank you for the suggestion. The exact way to manifest the flags came up in internal discussion. I actually proposed basically the approach you detail here (I wanted...

Hi @gneedle1 It depends on the type of experiment. If the barcodes are the same sample and you are trying to get at some other specific property (e.g. cell type...

I see, so in this case, each barcode corresponds to a specific cell. If you have sufficient coverage, you can split by barcode and make the call, it's really just...

Hi @SHuang-Broad Thank you for the report. We think the two items are linked and we are working on a patch that we plan to release to cover the issue.

Hi @Luosanmu, For your filtering question. We don't directly calculate many of the statistics in the INFO field for variant calling. We observe that the most effective way to adjust...

Thank you @Luosanmu I see. From your image, I think I understand why DeepVariant would make a REF call here. The variant in question is a 1-bp extension of a...

Hi @NIBIL401 Could I request a bit more information. When you say there are fewer variants, what are you comparing this to? I do note that you have BIN_VERSION=1.5.0, but...

Hi @NIBIL401 I don't see any other specific issues in your command. Without knowing more about the specific types of differences, it's difficult to give advice on what might be...

Hi @NIBIL401 I'm sorry, but without taking a look at the BAM file and the variants called or not called, it's quite difficult to say the reason why a variant...

Hi @Fred-07, As @akolesnikov mentions, the reason that the reads are re-aligned in this way has to do with some fundamental aspects of how alignment penalties work. The alignment method,...