google/deepvariant issues and pull requests

#888 - Call variant from bam file which includes methylation tags (MM/ML)

Issue - State: open - Opened by timizeng 5 days ago - 1 comment

#887 - Question about intermediate_results

Issue - State: closed - Opened by 0809zheng 8 days ago - 2 comments

#886 - D

Issue - State: open - Opened by desmodus1984 9 days ago - 1 comment

#885 - Discussion on Multi-GPU Training

Issue - State: closed - Opened by 0809zheng 12 days ago - 1 comment

#884 - Compatibility of DeepSomatic Tumor-Only Mode for Short-Read RNA-Seq without Control Sample

Issue - State: closed - Opened by Yousuk-Song 18 days ago - 1 comment

#883 - Running deepvariant within Nextflow DSL2

Issue - State: open - Opened by dbhayal9 19 days ago - 4 comments

#882 - adding acknowledgement for Maria

Pull Request - State: closed - Opened by lucasbrambrink 19 days ago

#881 - Deepvariant results quality filtration

Issue - State: closed - Opened by esraaelmligy 21 days ago - 5 comments

#880 - VAF != AD[1]/(AD[0]+AD[1])

Issue - State: closed - Opened by minw2828 22 days ago - 1 comment

#879 - Fatal Python error: Segmentation fault

Issue - State: closed - Opened by jellycatfish195 25 days ago - 8 comments

#878 - Retraining DeepVariant without trios data?

Issue - State: closed - Opened by desmodus1984 25 days ago - 9 comments

#877 - Fatal Python error: Aborted

Issue - State: closed - Opened by Yousuk-Song 28 days ago - 6 comments

#876 - No evaluation statistics for het and homalt calls during model training

Issue - State: closed - Opened by DanJeffries about 1 month ago - 13 comments

#875 - Mitochondial contig variants

Issue - State: closed - Opened by sounkou-bioinfo about 1 month ago - 2 comments

#874 - Deepvariant Structural Variants for ONT

Issue - State: closed - Opened by DineshRavindraRaju about 1 month ago - 1 comment

#873 - CPU and GPU using

Issue - State: closed - Opened by weiranmmm about 1 month ago - 2 comments

#872 - How do you see the future of CNN outside of human genomics?

Issue - State: closed - Opened by Axze-rgb about 1 month ago - 4 comments

#871 - Troubleshooting Dockerfile for DeepVariant on Mac M1: Issues with Bazel

Issue - State: closed - Opened by ghost about 1 month ago - 2 comments

#870 - [libprotobuf ERROR external/com_google_protobuf/src/google/protobuf/wire_format_lite.cc:584]

Issue - State: closed - Opened by alisamatisse about 1 month ago - 2 comments

#869 - No output vcf obtained from custom model

Issue - State: closed - Opened by bioinformaticaomicalabs about 1 month ago - 9 comments

#868 - No output files (VCFs) for all genome

Issue - State: closed - Opened by vera-gomes about 2 months ago - 7 comments

#867 - make_examples_core.py gets stuck on STAR aligned rnaseq BAM (deepvariant 1.6.1)

Issue - State: closed - Opened by melop about 2 months ago - 1 comment

#866 - Checkpoint "Model files do not exist" when testing custom model

Issue - State: closed - Opened by helizabeth1103 about 2 months ago - 2 comments

#865 - Running with Conda

Issue - State: closed - Opened by lynnjo about 2 months ago - 4 comments

#864 - Question about RNA-seq

Issue - State: closed - Opened by SirKuikka about 2 months ago - 5 comments

#863 - dealing with chimeric alignments

Issue - State: closed - Opened by alisamatisse about 2 months ago - 3 comments

#862 - Info Singularity

Issue - State: closed - Opened by gambalab about 2 months ago - 1 comment

#861 - DeepVariant Channel clarification

Issue - State: closed - Opened by ejc043 about 2 months ago - 2 comments

#860 - What is deepvariant trained on?

Issue - State: closed - Opened by ejc043 about 2 months ago - 3 comments

#859 - Source code compilation of DeepVariant failed

Issue - State: closed - Opened by Schroedingers0216 2 months ago - 3 comments

#858 - I have a question about training DeepVariant.

Issue - State: closed - Opened by pioneer-pi 2 months ago - 2 comments

#857 - AssertionError: Some objects had attributes which were not restored:

Issue - State: closed - Opened by xianyu0623 2 months ago - 4 comments

#856 - DeepVariant running slow

Issue - State: closed - Opened by DineshRavindraRaju 2 months ago - 1 comment

#855 - Program always run

Issue - State: closed - Opened by liukeweiaway 2 months ago - 3 comments

#854 - Memory issue while running deepvariant_1.6.0.sif with ONT_R104

Issue - State: closed - Opened by DineshRavindraRaju 2 months ago - 7 comments

#853 - Error while running tests on Calling variants in non-autosomal contigs

Issue - State: closed - Opened by poddarharsh15 2 months ago - 4 comments

#852 - I read DeepVariant essay and want to download some data.

Issue - State: closed - Opened by pioneer-pi 3 months ago - 4 comments

#851 - ValueError: Reference contigs span 3137161264 bases but only 63025520 bases (2.01%) were found in common among our input files. Check that the sources were created on a common genome reference build.

Issue - State: closed - Opened by pioneer-pi 3 months ago - 1 comment

#850 - No vcf output after running

Issue - State: closed - Opened by lok27395 3 months ago - 1 comment

#849 - Postprocess_variants.py ValueError: ptrue must be between zero and one: nan

Issue - State: closed - Opened by karoliinas 3 months ago - 12 comments

#848 - Why all the GT of the PASS variant site is 1/1? use deepsomatic

Issue - State: closed - Opened by DayTimeMouse 3 months ago - 1 comment

#847 - Deepvariant run too long and fails on giraffe output

Issue - State: closed - Opened by Han-Cao 3 months ago - 8 comments

#846 - I have a question about how deepvariant create the vcf files?

Issue - State: closed - Opened by pioneer-pi 3 months ago - 1 comment

#845 - AssertionError: Some objects had attributes which were not restored:

Issue - State: closed - Opened by esraaelmligy 3 months ago - 3 comments

#844 - google/deepvariant:1.5.0-gpu | google/deepvariant:1.6.1-gpu docker images run as CPU-only because they are using ancient CUDA 11.3.1

Issue - State: closed - Opened by s-batalov 3 months ago - 3 comments

#843 - DeepVariant Variant Allele Frequency

Issue - State: closed - Opened by Wasya-the-Wolf 3 months ago - 9 comments

#842 - data resources path

Issue - State: closed - Opened by zyxNo1 3 months ago - 1 comment

#841 - How to train deepvariant v1.6.1 on tpu?

Issue - State: closed - Opened by gambalab 3 months ago - 1 comment

#840 - Follow up to issue 797

Issue - State: closed - Opened by helizabeth1103 3 months ago - 3 comments

#839 - AttributeError issue

Issue - State: closed - Opened by hangy1 3 months ago - 10 comments

#838 - Deepvariant genotype

Issue - State: closed - Opened by MKaandemir 3 months ago - 7 comments

#837 - training on google engine

Issue - State: closed - Opened by gambalab 3 months ago - 2 comments

#836 - Indel calling for long read sequencing

Issue - State: closed - Opened by may199128 3 months ago - 4 comments

#835 - Cannot install latest DeepVariant via Conda

Issue - State: closed - Opened by lok27395 3 months ago - 4 comments

#834 - run DeepVariant on ARM64

Issue - State: closed - Opened by 0820LL 3 months ago - 2 comments

#833 - Error encountered while running on downsampled BAM

Issue - State: closed - Opened by snakesch 3 months ago - 3 comments

#832 - training with multi-gpu

Issue - State: closed - Opened by gambalab 4 months ago - 2 comments

#831 - A timeout error occurs

Issue - State: closed - Opened by sunqiangzai 4 months ago - 2 comments

#830 - google/deepvariant:1.6.1 docker says version 1.6.0

Issue - State: closed - Opened by fellen31 4 months ago - 7 comments

#829 - docker: invalid reference format.

Issue - State: closed - Opened by Jyoti-Mridha 4 months ago - 6 comments

#828 - Use haplotagged bam file with WES model type

Issue - State: closed - Opened by eaooms 4 months ago - 6 comments

#827 - any progress on somatic SNV calling?

Issue - State: closed - Opened by proukakis 4 months ago - 1 comment

#826 - gvcf with true depth and not (only) min_dp

Issue - State: closed - Opened by ESDeutekom 4 months ago - 5 comments

#825 - Fix male VCF after calling without --haploid_contigs="chrX,chrY" and/or --par_regions_bed parameters

Issue - State: closed - Opened by NourMarzouka 4 months ago - 2 comments

#824 - Homozygous GT value while IGV shows otherwise

Issue - State: closed - Opened by asalimih 4 months ago - 9 comments

#823 - Error while using deepvariant with a bam file that is phased

Issue - State: closed - Opened by eaooms 4 months ago - 4 comments

#822 - error while running deepvariant with a bam file with phasing information

Issue - State: closed - Opened by eaooms 4 months ago

#821 - Info ONT R10.4.1 data

Issue - State: closed - Opened by gambalab 5 months ago - 3 comments

#820 - CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected

Issue - State: closed - Opened by kunmonster 5 months ago - 10 comments

#819 - Issues with Incompatible TensorRT libraries in docker image google/deepvariant:latest-gpu and google/deepvariant:1.6.1-gpu

Issue - State: closed - Opened by nlopez94 5 months ago - 9 comments

#818 - postprocess_variants: Found multiple file patterns in input filename space

Issue - State: closed - Opened by MiWitt 5 months ago - 8 comments

#817 - [E::vcf_parse_format] Incorrect number of FORMAT fields at NC_059157.1:24900

Issue - State: closed - Opened by ilalab 5 months ago - 2 comments

#816 - haploid contigs and PAR region options for DeepTrio

Issue - State: closed - Opened by prasundutta87 5 months ago - 13 comments

#815 - Merging vcf files error with glnexus:v1.2.7

Issue - State: closed - Opened by poddarharsh15 5 months ago - 6 comments

#814 - Question about the time it takes for VC analysis

Issue - State: closed - Opened by bkurtoglu 5 months ago - 5 comments

#813 - question for INDEL variant calling

Issue - State: closed - Opened by sophienguyen01 5 months ago - 14 comments

#812 - Dynamic cast failed

Issue - State: closed - Opened by Carl-labhub 5 months ago - 6 comments

#811 - Merging gvcf with GLnexus introduces non-zero heterozygous PL in hemizygous PAR

Issue - State: open - Opened by ASLeonard 5 months ago - 3 comments

#810 - Output files are missing after running deepvariant.

Issue - State: closed - Opened by githubtefo 5 months ago - 10 comments

#804 - BrokenPipeErro during postprocess_variants

Issue - State: closed - Opened by LogCrab 6 months ago - 9 comments

#779 - DeepTrio from 1.6.0 : how to isolate de novo calls from trio VCF ?

Issue - State: closed - Opened by francois-lecoquierre 7 months ago - 4 comments

#763 - Variant calls after local realignment : is it the most accurate ?

Issue - State: closed - Opened by Fred-07 9 months ago - 6 comments

#727 - There is something wrong while I building DeepVariant from source

Issue - State: closed - Opened by pioneer-pi 11 months ago - 4 comments

#534 - Should DV be re-trained with new human T2T reference

Issue - State: closed - Opened by SHuang-Broad over 2 years ago - 7 comments

#347 - CLR PacBio data

Issue - State: closed - Opened by jdmontenegro about 4 years ago - 4 comments

#181 - ref variable path is not being found in deep variant run

Issue - State: closed - Opened by ashraf123456789 over 5 years ago - 6 comments

#109 - DeepVariant miss the truth variant gene site

Issue - State: closed - Opened by ssm0808 almost 6 years ago - 11 comments

#100 - Build options for Tensorflow in the docker image

Issue - State: closed - Opened by junehawk almost 6 years ago - 1 comment

#99 - ValueError: Data loss: Expected mtid >= 0 as mate is supposedly mapped

Issue - State: closed - Opened by zyxue almost 6 years ago - 38 comments

#98 - Errors when building with Ubuntu 18.04

Issue - State: closed - Opened by vinisalazar about 6 years ago - 14 comments

#97 - Old style exceptions --> new style for Python 3

Pull Request - State: closed - Opened by cclauss about 6 years ago - 1 comment

#96 - Error: validating pipeline: zones and regions cannot be specified together

Issue - State: closed - Opened by ShrutiMarwaha about 6 years ago - 4 comments

GitHub / google/deepvariant issues and pull requests