Usage: sga filterBAM [OPTION] ... ASQGFILE BAMFILE Discard mate-pair alignments from a BAM file that are potentially erroneous --help display this help and exit -v, --verbose display verbose output -a, --asqg=FILE load an asqg file and filter pairs that are shorter than --max-distance -d, --max-distance=LEN search the graph for a path completing the mate-pair fragment. If the path is less than LEN then the pair will be discarded. -e, --error-rate=F filter out pairs where one read has an error rate higher than F (default: no filter) -q, --min-quality=F filter out pairs where one read has mapping quality less than F (default: 10) -o, --out-bam=FILE write the filtered reads to FILE -p, --prefix=STR load the FM-index with prefix STR -x, --max-kmer-depth=N filter out pairs that contain a kmer that has been seen in the FM-index more than N times -c, --mate-contamination filter out pairs aligning with FR orientation, which may be contiminates in a mate pair library Report bugs to js18@sanger.ac.uk