samtools
samtools
TLDR
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]
