Linux command
samtools 命令
文件
复制后可按需替换文件名、目录或参数。
常用示例
View BAM file
samtools view [alignment.bam]
Convert SAM to BAM
samtools view -b [alignment.sam] -o [alignment.bam]
Sort BAM file
samtools sort [input.bam] -o [sorted.bam]
Index BAM file
samtools index [sorted.bam]
View specific region
samtools view [sorted.bam] [chr1:1000-2000]
Count alignments
samtools view -c [alignment.bam]
Generate statistics
samtools flagstat [alignment.bam]
Merge BAM files
samtools merge [output.bam] [input1.bam] [input2.bam]
说明
samtools manipulates alignments in SAM (Sequence Alignment/Map) format and its binary equivalent BAM. It's essential for next-generation sequencing data analysis. SAM/BAM files contain sequence reads aligned to reference genomes. Each record includes read name, position, mapping quality, CIGAR string (alignment operations), and optional tags. The view command converts between formats and filters alignments. Sorted BAM files with indices enable random access to genomic regions. Most downstream tools require sorted, indexed BAM. Statistics commands (flagstat, stats, idxstats) summarize alignment characteristics: mapping rates, insert sizes, coverage distributions. These quality metrics guide analysis decisions. Pileup output (mpileup) aggregates alignments at each position for variant calling. Coverage commands calculate read depth across regions. CRAM format provides better compression than BAM with reference-based encoding. Samtools handles CRAM transparently.
参数
- view
- View/convert SAM/BAM/CRAM.
- sort
- Sort alignments.
- index
- Create BAM index.
- merge
- Merge sorted files.
- flagstat
- Statistics from FLAG field.
- stats
- Comprehensive statistics.
- idxstats
- Per-reference statistics.
- faidx
- Index FASTA file.
- depth
- Compute depth at each position.
- mpileup
- Generate pileup for variants.
- coverage
- Calculate coverage statistics.
- fastq
- Extract FASTQ from BAM.
- collate
- Shuffle and group alignments by name.
- calmd
- Recalculate MD/NM tags.
- -b
- Output BAM format.
- -S
- Input is SAM (ignored, format is auto-detected).
- -o _FILE_
- Output file.
- -@ _NUM_, --threads _NUM_
- Number of threads.
- -f _FLAGS_
- Only include reads with FLAGS.
- -F _FLAGS_
- Exclude reads with FLAGS.
- -q _MAPQ_
- Minimum mapping quality.
- -h
- Include header.
FAQ
What is the samtools command used for?
samtools manipulates alignments in SAM (Sequence Alignment/Map) format and its binary equivalent BAM. It's essential for next-generation sequencing data analysis. SAM/BAM files contain sequence reads aligned to reference genomes. Each record includes read name, position, mapping quality, CIGAR string (alignment operations), and optional tags. The view command converts between formats and filters alignments. Sorted BAM files with indices enable random access to genomic regions. Most downstream tools require sorted, indexed BAM. Statistics commands (flagstat, stats, idxstats) summarize alignment characteristics: mapping rates, insert sizes, coverage distributions. These quality metrics guide analysis decisions. Pileup output (mpileup) aggregates alignments at each position for variant calling. Coverage commands calculate read depth across regions. CRAM format provides better compression than BAM with reference-based encoding. Samtools handles CRAM transparently.
How do I run a basic samtools example?
Run `samtools view [alignment.bam]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does view do in samtools?
View/convert SAM/BAM/CRAM.