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.
Hello, Noticed this issue with your tool DeepTrio regarding the representation of hemizygous variants in the non-pseudoautosomal (PAR) X-chromosome. This may be fixed now in 1.3? If so ignore this,...
I understand that PRs are not performed on github. So, I just wanted to recommend/discuss some potential changes for the shuffle_tfrecords_beam.py script to enable running it with SparkRunner (PortableRunner). Without...
Hi, I am wondering if the DV team has done an evaluation on how the availability of BAQ (the `BQ:Z:...` tag) affects the quality of calls generated from HiFi reads....
**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.4/docs/FAQ.md**: **Describe the issue:** According to the running log: the setlocale failed when trying to change LC_ALL to 'en_US.UTF-8' **Setup** - Operating system: CentOS7 -...
**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.4/docs/FAQ.md**: Yes **Describe the issue:** At the call_variants.py step, running into error that tensorflow.python.framework.errors_impl.DataLossError: truncated record at 19179998357' failed with EOF reached (A clear and...
**Describe the issue:** I previously used the following PopVCF [model.ckpt](https://console.cloud.google.com/storage/browser/brain-genomics-public/research/allele_frequency/pretrained_model_WGS;tab=objects?pli=1&prefix=&forceOnObjectsSortingFiltering=false) with `run_deepvariant` v.1.1 while including a PopVCF channel during `make_examples`. However, that model does not include a channel for `insert_size`...
Hi I have used the following script to run deepvariant (v1.6.0) on WGS samples. ``` bash singularity exec -H $(pwd) docker://google/deepvariant:1.6.0 \ /opt/deepvariant/bin/run_deepvariant \ --model_type=${6} \ --ref=./human_g1k_v37_decoy.fasta \ --reads=./${2}_md.recal.cram \...
I have run the following command for RNA seq data and the output vcf size is very less and important variants are missing BIN_VERSION="1.5.0" ```dockerfile docker run \ -v "$(pwd):$(pwd)"...
Hi, I followed the instructions on deepvariant quick start (https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md) to create deepvariant_1.6.0.sif and deepvariant_1.6.0-gpu.sif successfully using apptainer. Then, I followed the complete genomics T7 case study (https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-complete-t7-case-study.md) to have...
