Description

High-performance VCF to PostgreSQL loader using asyncpg for bulk variant ingestion

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’, family:‘FAM001’, affected:true ]

vcf{:bash}

:file

Annotated VCF file containing variants to load

*.{vcf,vcf.gz}

tbi{:bash}

:file

Tabix index for the VCF file

*.tbi

db_host{:bash}

:string

PostgreSQL server hostname or IP address

db_port{:bash}

:integer

PostgreSQL server port (default 5432)

db_name{:bash}

:string

Target database name

db_user{:bash}

:string

Database username for authentication

db_schema{:bash}

:string

Target schema for variant tables (default public)

Output

name:type
description
pattern

report{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’ ]

*.load_report.json{:bash}

:file

JSON report with loading statistics including variant counts, elapsed time, and throughput metrics

*.load_report.json

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’ ]

*.load.log{:bash}

:file

Detailed loading log with any warnings or errors

*.load.log

row_count{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’ ]

ROWS_LOADED{:bash}

:integer

Number of variant records successfully loaded

versions_vcfpgloader{:bash}

${task.process}{:bash}

:string

The name of the process

vcf-pg-loader{:bash}

:string

The name of the tool

vcf-pg-loader --version | sed 's/.*version //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

vcf-pg-loader{:bash}

:string

The name of the tool

vcf-pg-loader --version | sed 's/.*version //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

vcf-pg-loader
MIT

High-throughput async PostgreSQL VCF loader using cyvcf2 and asyncpg. Supports variant normalization, multi-allelic decomposition, and clinical-grade audit trails.

args_id: $args
github.com/Zacharyr41/vcf-pg-loader github.com/Zacharyr41/vcf-pg-loader#readme https://github.com/Zacharyr41/vcf-pg-loader
maintainer
Github user Zacharyr41
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