Changes

  qplot --rerefence reference.fa --windowsize winsize --create_gc reference.gc

  qplot --rerefence reference.fa --windowsize winsize --create_gc reference.gc

''Note'': Before running qplot, it is critical to check how the chromosome numbers are coded. Some BAM/SAM files use just numbers, others use chr + numbers. '''You need to make sure that the chromosome numbers from the reference and dbSNP are consistent with the BAM/SAM file.'''

''Note'': Before running qplot, it is critical to check how the chromosome names are coded. Some BAM/SAM files use just numbers, others use chr + numbers. '''You need to make sure that the chromosome names from the reference and dbSNP are consistent with the BAM/SAM files.'''

== Parameters ==

== Parameters ==