bam2cfg - generate analysis configure files


perl bam_files


-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