Table 1.

BamTools command-line toolkit

Utility	Description
convert	Converts between BAM and a number of other formats.
count	Prints number of alignments in BAM file(s).
coverage	Prints coverage information from a BAM file.
filter	Filters BAM file(s) based on user-specified criteria.
header	Prints BAM header information.
index	Generates index for BAM file (either BAI or BTI).
merge	Merges multiple BAM files into single file.
sort	Sorts the BAM file.
split	Splits a BAM file into multiple files, based on some criteria.
stats	Prints general statistics from input BAM file(s).