SCI Skills

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

bio-variant-calling

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

Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.

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

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

  • Call SNPs 、 indels ，面向 aligned reads ，使用 bcftools。
  • bcftools mpileup -f reference.fa -b bams.txt | bcftools call -mv -o variants.vcf。

原始文档

SKILL.md 摘录

bcftools mpileup + call

Goal: Detect SNPs and indels from aligned reads using the bcftools pileup-and-call pipeline.

Approach: Generate per-position pileup likelihoods with mpileup, then call genotypes with the multiallelic caller.

"Call variants from my BAM file" → Generate genotype likelihoods from aligned reads and identify variant sites using a Bayesian caller.

mpileup Options

Goal: Control pileup generation with quality thresholds, annotations, and region restrictions.

Approach: Set minimum mapping/base quality, request specific FORMAT/INFO tags, and restrict to target regions.

Calling Models

FlagModelUse Case
-mMultiallelic callerDefault, recommended
-cConsensus callerLegacy, single sample

适用场景

  • 适合在detecting variants ，面向 BAM files 或 generating VCF ，面向 alignments时使用。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

  • vcf-basics - View and query resulting VCF
  • filtering-best-practices - Filter variants by quality
  • variant-normalization - Normalize indels
  • alignment-files/pileup-generation - Alternative pileup generation

相关技能

相关技能

返回目录
AR
数据与复现临床医学与医药

armored-cart-design-agent

Design armored CAR-T cells with cytokine payloads and resistance mechanisms.

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
AR
数据与复现临床医学与医药

arxiv-search

Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic sea…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
AU
数据与复现临床医学与医药

autonomous-oncology-agent

Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis gene…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
BI
数据与复现临床医学与医药

bio-cfdna-preprocessing

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看