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Questions tagged [google-genomics]

Google Genomics provides an API for working with genomic data on Google's infrastructure.

Google Genomics provides an API for working with genomic data on Google's infrastructure. For more information see:

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Pre-emptible machines on genomics pipeline

I tried running thousands of machines using the genomics pipeline using the preemptible flag in v2alpha1 JSON mapping. Even though the machines were preemptible - a lot of workers were using up persistent disk space while not even having started. …
Bharathwaj Raghu
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gcloud.alpha.genomics.pipelines.run - No such file or directory: 'wdl_pipeline.yaml'

I am trying to run the GATK best practices pipeline in google cloud and get below error here's the gcloud command: gcloud alpha genomics pipelines run \ --pipeline-file wdl_pipeline.yaml \ --regions us-central1 \ --inputs-from-file…
Sethuramalingam Sundaram
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How to calculate the cost (bill) of a Google Cloud Genomics Pipeline

I'm using the Cromwell engine on Google Cloud, which submits pipeline run requests: https://cloud.google.com/genomics/reference/rest/v1alpha2/pipelines/run. Once the pipelines have finished, I am then able to find the Google Cloud operations…
Migwell
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Running DeepVariant on GRCh38 Whole Exome Sequence

I'm trying to run DeepVariant on my BAM file to produce a VCF. I have the following questions: 1 - The alignment is in GRCh38, which model should I use. Can I use the standard whole exome sequence model?…
user491880
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Error on Google Cloud - Genomics: "API solution not found with service name: genomics"

I am completely new to the HPC and Google Cloud (I just signed for a trial account) . My Idea is to perform a RNAseq analysis (9 samples paired, 18 fastQ files), Mainly I want to perform the FastQC and the mapping trying different aligments.…
FJ_Bioinf
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Access random line in large file on Google Cloud Storage

I'm trying to read a random line out of a large file stored in a public cloud storage bucket. My understanding is that I can't do this with gsutil and have looked into FUSE but am not sure it will fill my use…
user491880
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How to do inheritance / transmission queries in BigQuery Variant Schema

The Variant Schema used by Google Genomics Variant Transform pipelines represents genotypes as nested records in BigQuery - for example: (from:…
user553965
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alternative of jbrowse on centos

Is there an alternative Software of JBrowse (on Centos6). I need to integrate one into my webpage, but jbrowse is giving error of zlib while installing PerlIO::gzip. Although all related modules…
onkar
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How to convert fastq to uBAM with picard dock on google cloud

I have been trying to convert my fastq files on google cloud to uBAM files but no success so far. Here is code I used: dsub \ --project projectID \ --zones "us-central1-*" \ --logging gs://bucket/logging \ --image broadinstitute/picard \ --command…
Bingley
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dsub: google cloud error ("exit status 141")

I was trying to run some whole genome sequencing samples on google cloud using dsub. The dsub commands work ok for some samples, but not others. I have tried reducing the number of parallel threads, increasing the memory and disk, but it still…
brian
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How is it possible to export a Cloud Genomics variantset to BigQuery now that varientsets.export has been deprecated?

I have loaded a variantset into Cloud Genomics and am attempting to export it to BigQuery. The first approach I tried was to use a pipeline as detailed here: https://cloud.google.com/genomics/docs/how-tos/load-variants However, 20 minutes into the…
EVMPMOArchitect
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Google genomics bigQuery difference tables data description

I would like read all the calls in a specific region of the genome. regardless of the genotype (equal to the reference genome or alternate, coding or non coding region). Assuming that all genome was sequenced. Which of the following tables should I…
eilalan
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googlegenomics: dsub error with pipelines-api-examples/fastqc example

I was trying to follow the fastqc example given in googlegenomics/pipelines-api-examples. However, when I try to re-produce the example with my projectID and bucketID, I get an error: | => dsub --project my_project_ID --logging…
bsmith
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Why are Google Pipeline VM instances hanging indefinitely?

I am using Dockerflow to run parallel tasks through the Google Pipelines API on Google Cloud Platform. I started a single-step task running 1389 VMs in parallel and found that 233 of the VMs were apparently doing nothing and hanging indefinitely. I…
Paul Billing-Ross
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How to enable the "late" version package in R (version higher into the package)- function/package "tracks"?

I tried to use the function/package "tracks", in R, but the version is not compatible. First, I thought that this function be of package "ggbio", but I installed this and don't running. I will use this function/package for merge two graphs, will be…
Amanda Botelho Alvarenga
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