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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-alignment-filtering

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

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

OpenClawNanoClaw分析处理复现实验bio-alignment-filtering🧠 bioos extended suitebioos extended bioinformatics suitefilter

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-filtering

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

  • Filter alignments by flags，quality，、 regions ，使用 samtools 、 pysam。
  • samtools view -F 3332 -q 30 -o filtered.bam input.bam。

原始文档

SKILL.md 摘录

Filter Flags

OptionDescription
-f FLAGInclude reads with ALL bits set
-F FLAGExclude reads with ANY bits set
-G FLAGExclude reads with ALL bits set
-q MAPQMinimum mapping quality
-L BEDInclude reads overlapping regions

Common FLAG Values

FlagHexMeaning
10x1Paired
20x2Proper pair
40x4Unmapped
80x8Mate unmapped
160x10Reverse strand
320x20Mate reverse strand
640x40First in pair (read1)
1280x80Second in pair (read2)
2560x100Secondary alignment
5120x200Failed QC
10240x400Duplicate
20480x800Supplementary

Keep Only Primary Alignments

samtools view -F 256 -F 2048 -o primary.bam input.bam

适用场景

  • Use bio-alignment-filtering ，用于 genomics 、 bioinformatics workflows。
  • Apply bio-alignment-filtering 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

  • sam-bam-basics - View and understand alignment files
  • alignment-sorting - Sort before/after filtering
  • alignment-indexing - Required for region filtering
  • duplicate-handling - Mark duplicates before filtering
  • bam-statistics - Check filter effects

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