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/doc/samtools.html.

• Convert a SAM input file to BAM stream and save to file:

samtools view -S {{[-b|--bam]}} {{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|--with-header]}} - 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]}} {{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}}