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