samtools
Verified for current stable LTS
Samtools Commands
Samtools command syntax with verified terminal examples.
Commands
8 commands for Samtools
samtools Operations
Samtools Command: Convert Sam To Bam
samtools view -S -b <input.sam> > <output.bam> samtools Operations
Samtools Command: Count Alignments Per Chromosome
samtools idxstats <sorted_indexed_input> samtools Operations
Samtools Command: Index Sorted Bam
samtools index <sorted_input.bam> samtools Operations
Samtools Command: Merge Multiple Files
samtools merge <output> <input1 input2 ...> samtools Operations
Samtools Command: Print Alignment Statistics
samtools flagstat <sorted_input> samtools HTTP
Samtools Command: Print Sam Header And Reads
<other_command> | samtools view -h - chromosome:start-end samtools Operations
Samtools Command: Sort Bam File
samtools sort <input> -o <output.bam> samtools Operations
Samtools Command: Split File By Read Groups
samtools split <merged_input> Suggest a Samtools Command
Submit missing workflows, corrections, or verified alternatives for this tool.
FAQ
Coverage: Focused examples for common Samtools workflows.
Verified version: current stable LTS.
Verification: Test commands in a disposable workspace and submit notes for edge cases.