数据与复现临床医学与医药FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-variant-calling-deepvariant

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller.

OpenClawNanoClaw分析处理复现实验bio-variant-calling-deepvariant🧬 bioinformatics (gptomics bio-* suite)bioinformatics — clinical databases & variant analysisdeep

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-calling-deepvariant

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

docker pull google/deepvariant：1.6.1-gpu。
用于 bam in *.bam；do sample=$(basename $bam.bam) docker run -v "${PWD}：/data" google/deepvariant：1.6.1 \ /opt/deepvariant/bin/run_deepvariant \ --model_type=WGS \ --ref=/data/reference.fa \ --reads=/data/$bam \ --output_vcf=/data/${sample}.vcf.gz \ --output_gvcf=/data/${sample}.g.vcf.gz \ --num_shards=16 done。

原始文档

SKILL.md 摘录

Installation

Goal: Install DeepVariant via Docker or Singularity container.

Approach: Pull the pre-built container image matching the target platform (CPU or GPU).

Docker (Recommended)

docker pull google/deepvariant:1.6.1

## Basic Usage

**Goal:** Call germline variants from aligned reads using DeepVariant's deep learning model.

**Approach:** Run the all-in-one `run_deepvariant` wrapper specifying model type, reference, reads, and output paths.

**"Call variants with DeepVariant"** → Convert aligned read pileups into image tensors, classify with a CNN, and output genotyped VCF.