Changes

* --reference

* --reference

** The reference genome is the same as karma reference genome. If the index files do not exist, qplot will create the index files using the input reference fasta file.

 

The reference genome is the same as karma reference genome. If the index files do not exist, qplot will create the index files using the input reference fasta file.

* --dbsnp

* --dbsnp

This file has two columns. First column is the chromosome name wich have to be consistent with the reference created above

 

This file has two columns. First column is the chromosome name wich have to be consistent with the reference created above.

* --gccontent

* --gccontent

Although GC content can be calculated on fly each time, it is much more efficient to load a precomputed GC content from a file. To generate the file, use the following command

Although GC content can be calculated on the fly each time, it is much more efficient to load a precomputed GC content from a file. To generate the file, use the following command

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

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

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

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

== Parameters ==

== Parameters ==