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