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Welcome to the bamsifter wiki!

Bamsifter is a small command line utility to downsample a sam/bam file to a given max coverge using htslib. It assumes the input file is sorted and outputs in the same format as the input.

bamsifter [-c max_coverage] [-o output_filename] [-i max_identical_cigar] file_to_process

The options available are the following:
-c: Max coverage target value (coverage can get higher if max coverage has been hit but the paired read of a previously selected read is encountered).
-o: Output file name. Default is to stdout.
-i: Max number of reads with an identical cigar starting at the some position to keep.