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Tools for handling high-throughput sequencing (genomics) data. Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format. More information:
  • 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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