SCI Skills

CN Directory
数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现
BI

bio-pileup-generation

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

Generate base-level pileup from BAM for variant calling and coverage.

OpenClawNanoClaw分析处理复现实验bio-pileup-generation🧠 bioos extended suitebioos extended bioinformatics suitegenerate

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pileup-generation

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

  • 生成 pileup data ，用于 variant calling 、 position-level analysis。
  • samtools mpileup -f reference.fa -d 1000 input.bam。

原始文档

SKILL.md 摘录

What is Pileup?

Pileup shows all reads covering each position in the reference, used for:

  • Variant calling (with bcftools)
  • Coverage analysis
  • Allele frequency calculation
  • SNP/indel detection

Output Format

Text pileup format (6 columns per sample):

ColumnDescription
1Chromosome
2Position (1-based)
3Reference base
4Read depth
5Read bases
6Base qualities

Read Bases Encoding

SymbolMeaning
.Match on forward strand
,Match on reverse strand
ACGTMismatch (uppercase = forward)
acgtMismatch (lowercase = reverse)
^QStart of read (Q = MAPQ as ASCII)
$End of read
+NNNInsertion of N bases
-NNNDeletion of N bases
*Deleted base
> / <Reference skip (intron)

适用场景

  • Use bio-pileup-generation ，用于 genomics 、 bioinformatics workflows。
  • Apply bio-pileup-generation to sequencing，variant，或 omics analysis tasks。

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

  • alignment-filtering - Filter BAM before pileup
  • reference-operations - Index reference for pileup
  • bam-statistics - depth command for coverage
  • variant-calling - bcftools call from pileup

相关技能

相关技能

返回目录
AG
数据与复现生物信息与基因组学

agent-browser

Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extr…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
AL
数据与复现生物信息与基因组学

alpha-vantage

Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ t…

Claude Code分析处理
K-Dense-AI/claude-scientific-skills查看
BI
数据与复现生物信息与基因组学

bio-alignment-filtering

Filter alignments by flag, quality, region, or paired status.

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
BI
数据与复现生物信息与基因组学

bio-alignment-indexing

Index BAM/CRAM files with samtools index for random access.

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