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samtools

 
Tools for handling high-throughput sequencing (genomics) data. Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format. More information: https://www.htslib.org.
 
  • Convert a SAM input file to BAM stream and save to file:
     
    samtools view -S -b {{input.sam}} > {{output.bam}}
     
  • Take input from stdin (-) and print the SAM header and any reads overlapping a specific region to stdout:
     
    {{other_command}} | samtools view -h - chromosome:start-end
     
  • Sort file and save to BAM (the output format is automatically determined from the output file's extension):
     
    samtools sort {{input}} -o {{output.bam}}
     
  • Index a sorted BAM file (creates {{sorted_input.bam.bai}}):
     
    samtools index {{sorted_input.bam}}
     
  • Print alignment statistics about a file:
     
    samtools flagstat {{sorted_input}}
     
  • Count alignments to each index (chromosome / contig):
     
    samtools idxstats {{sorted_indexed_input}}
     
  • Merge multiple files:
     
    samtools merge {{output}} {{input1 input2 …}}
     
  • Split input file according to read groups:
     
    samtools split {{merged_input}}

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