Error while using deepvariant with a bam file that is phased about deepvariant HOT 4 CLOSED

Hi @eaooms ,
Starting in DeepVariant v1.4.0, wehave our read haplotagging built in.

To use the flag you mentioned, please use BIN_VERSION=1.3.0. You can read:
https://github.com/google/deepvariant/blob/r1.3/docs/deepvariant-pacbio-model-case-study.md

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I'll close this issue now. Please feel free to open as needed.

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Thank u for the quick respond

Where can i find what Deepvariant does with the phasing information in the bam file?

Because it is still a bit unclear to me what Deepvariant does with the added HP channel that u get from Whatshap haplotag mentioned in the case study ( https://google.github.io/deepvariant/posts/2021-02-08-the-haplotype-channel/ )

In what way does it influence the variant caller in making its decisions for picking the found variants?

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Hi @eaooms ,
DeepVariant adds an additional channel to represent the HP information.
If you have some intermediate output of make_examples available, you can try using https://github.com/google/deepvariant/blob/r1.6.1/docs/show-examples.md to visualize them.

In addition to the blog post, this preprint might provide the information that you need: https://doi.org/10.1101/2023.09.07.556731

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