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}}