bam2cfg - generate analysis configure files


Usage


perl bam2cfg.pl bam_files

Options: 


         -q INT      Minumum mapping quality [35]

         -m          Using mapping quality instead of alternative ampping quality

         -s          Minimal mean insert size [50]

         -C          Change default system from Illumina to SOLiD

         -c FLOAT    Cut off in unit of standard deviation [4]

         -n INT      Number of observation required to estimate mean and s.d. insert size [10000]

         -v FLOAT    Cutoff on coefficients of variation [1]

         -f STRING   A two column tab-delimited text file (RG, LIB) specify the RG=>LIB mapping, useful when BAM header is incomplete

         -b INT      Number of bins in the histogram [50]

         -g          Output mapping flag distribution

         -h          Plot insert size histogram for each BAM library