GenomeComb
cg sam_clipamplicons ?options? ampliconsfile ?sourcefile? ?resultfile?
Clip primers from aligned sequences in a sam file (by changing bases to N and quality to 0) given a set of target amplicons.
cg sam_clipamplicons clips primers from aligned sequences in a sam file (by changing bases to N and quality to 0) given a set of target amplicons.
sourcefile can be in sam, bam or cram format. (in case of cram, the -refseq option must be given). The format is deduced from the file extension. If sourcefile is not given or "-", the input data is taken from stdin. In this case, it must be in sam format, unless the option -inputformat is used to specify another input format.
resultfile can also be in sam, bam or cram format. When sent to stdout (resultfile absent or "-") the format defaults to sam, unless changed using the -outputformat option.
Conversion