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* --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
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 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 -r reference.fa -w windowSize -o 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 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.'''
