googlegenomics/gcp-variant-transforms

Issues

• was `cloud-lifesciences` taken off `gcr.io` before the deadline?

  #721 opened 23 days ago by purajit
  7

• subnetwork flag to use network/subnet outside the project where dataflow runs in

  #720 opened a year ago by bujiazhang
  0

• support for newer version than python 3.7

  #719 opened 2 years ago by mizue31g
  0

• VCF to BQ via docker keeps failing

  #718 opened 3 years ago by mkahn5
  1

• AnnotateShards not producing **vep_output.vcf

  #717 opened 3 years ago by KevinDuringWork
  3

• VCF to BQ Timeout Issue

  #699 opened 3 years ago by adaykin
  4

• Add a flag to specify the "pipeline mode" (SMALL, MEDIUM, or LARGE)

  #659 opened 3 years ago by mbookman
  7

• Update `vep_runner.py` to use Life Sciences `v2beta` API

  #650 opened 3 years ago by mbookman
  0

• Update the VEP release used for annotations

  #665 opened 3 years ago by mbookman
  1

• unable to pull from pypi.org when running under VPC SC

  #705 opened 3 years ago by lawrenae
  0

• pyYAML 6.0 incompatability

  #704 opened 3 years ago by james-lawlor
  1

• flatten null repeated column

  #706 opened 3 years ago by dbaid
  0

• Network parameter not being read

  #696 opened 4 years ago by abalter
  27

• The MISSING_GENOTYPE_VALUE value of -1 can conflict with genotype values that are in a VCF (scalar vs. list)

  #703 opened 3 years ago by adaykin
  0

• Dataflow workers use private IP addresses

  #630 opened 5 years ago by samanvp
  3

• vcf_to_bq running with --run_annotation_pipeline fails to find **_vep_output.vcf files

  #655 opened 4 years ago by TomGardner
  2

• move_hom_ref_calls python error

  #695 opened 4 years ago by james-lawlor
  1

• off by 1 error?

  #694 opened 4 years ago by bradmonk
  3

• Add a flag to preserve the call.name field

  #660 opened 4 years ago by mbookman
  9

• Add an option to disable sharding

  #679 opened 4 years ago by arostamianfar
  0

• Fix deploy_and_run_tests.sh to be locally runnable.

  #666 opened 4 years ago by tneymanov
  0

• Enabling --save_main_session pipeline option in our pipelines.

  #667 opened 4 years ago by tneymanov
  1

• Document how to use Dataflow Flexible Resource Scheduling to save on Cloud cost

  #662 opened 4 years ago by mbookman
  0

• Add a flag to omit homozygous reference calls on vcf_to_bq import

  #661 opened 4 years ago by mbookman
  0

• merge_header pipeline should not run when --representative_header_file is set

  #658 opened 4 years ago by mbookman
  0

• Add timestamps to the logging messages

  #651 opened 4 years ago by samanvp
  0

• Move Avro related items out of bigquery_util.py

  #644 opened 4 years ago by samanvp
  0

• Proper use of const values defined in vcf_header_io.py

  #643 opened 4 years ago by samanvp
  0

• Sharding config with "Partition Range Start"

  #641 opened 4 years ago by samanvp
  0

• Sample lookup optimized tables with `--append` flag

  #607 opened 5 years ago by samanvp
  0

• Store VCF headers along with Avro files

  #640 opened 4 years ago by samanvp
  0

• Rollback sample info if fail happens before pipeline is ran.

  #581 opened 4 years ago by tneymanov
  1

• Modify bq_to_vcf integration tests to verify default 1-based coordinate

  #637 opened 4 years ago by samanvp
  0

• Update Platinum dataset

  #629 opened 5 years ago by samanvp
  0

• Scaling to ~1000 samples fails

  #618 opened 5 years ago by samesense
  1

• More rigorous integration tests for sample optimized tables

  #617 opened 5 years ago by samanvp
  0

• pysam 0.16.0 halts with malformed VCF file

  #613 opened 5 years ago by samanvp
  0

• Organize `bigquery_util`module

  #598 opened 5 years ago by samanvp
  0

• Do not add FORMAT in bq_to_vcf flow if there are no samples in the selected regions.

  #592 opened 5 years ago by tneymanov
  0

• Failed Precondition error

  #591 opened 5 years ago by marcelokauffman
  4

• Remove Base parser class for VT codebase.

  #589 opened 5 years ago by tneymanov
  0

• Use BigQuery API to create integer range partition tables

  #582 opened 5 years ago by samanvp
  1

• unexpected status 1 was not ignored

  #578 opened 5 years ago by raldponsua
  6

• DataFlow suggestion

  #570 opened 5 years ago by Rokshan2016
  1

• Enable bq_to_vcf to drop irrelevant variants when `--sample_names` is set

  #565 opened 5 years ago by samanvp
  1

• Add a new merging strategy: aggregate alleles

  #563 opened 5 years ago by samanvp
  0

• No need to use `reference_name` in merge key

  #562 opened 5 years ago by samanvp
  0

• Read VCF File From GCS Bucket

  #547 opened 5 years ago by Rokshan2016
  2

• Implement a new BigQuery sink

  #549 opened 5 years ago by tneymanov
  1

• Using data from GCS Bucket

  #546 opened 5 years ago by chaeyoung-lee
  1