deepvariant
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google
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Fix male VCF after calling without --haploid_contigs="chrX,chrY" and/or --par_regions_bed parameters
If I generated a VCF file for a trio (with a father using deeptrio) or a solo male (using deepvariant) without --haploid_contigs="chrX,chrY" and/or --par_regions_bed parameters. Can I fix the VCF...
Sorry to bother, but could you please provide me with the original path for downloading the data in the exome case study? I am interested in exploring some related data....
Hello, Previously I had an issue where the parameters I was using were not producing checkpoints in the model training step. I know that choosing parameters has a component of...
**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**: Yes **Describe the issue:** **Setup** - Operating system: Ubuntu 20.04.6 LTS - DeepVariant version: 1.6 - Installation method (Docker, built from source, etc.): singularity...
Hi, Thanks for the great tool. I got the following variant lines. I wonder how should I handle them since they are germline calls. The input bam consist of only...
**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**: **Describe the issue:** When I check the version of google/deepvariant:1.6.1 it says 1.6.0, and the docker image has `ENV VERSION=1.6.0` ``` docker run google/deepvariant:1.6.1...
Describe the issue: We are currently using two different long-read sequencing systems: PacBio Direct and PacBio Capture. We are encountering two specific issues: 1. **PacBio Direct Data (top track)**: Despite...
**Describe the issue:** Cannot install latest DeepVariant via Conda in my new environment Error prompts, similar to that of #736 If having everything in default, I can have python=2.7 and...
I need to run DeepVariant on ARM64 architecture. Is there an available Docker image for this, or what steps should I take to achieve it? Thank you ~
Hello DV team, and thanks for creating such a great tool! I am currently trying to retrain the wgs model for a new species (a fish) however, during training, I...
