bamPEFragmentSizeΒΆ
Given a BAM file, several regions are sampled depending on the size of the genome and number of processors to estimate the paired-end fragment length. Properly paired reads are preferred for computation.
usage: bamPEFragmentSize [-h] [--histogram FILE] [--numberOfProcessors INT]
[--plotTitle PLOTTITLE] [--verbose] [--version]
bam-file
- Positional arguments:
bam BAM file to process - optional arguments
--histogram, -hist Save a .png file with a histogram of the fragment length distribution. --numberOfProcessors=1, -p=1 Number of processors to use. The default is to use 1. --plotTitle=, -T= Title of the plot, to be printed on top of the generated image. Leave blank for no title. --verbose=False Set if processing data messages are wanted. --version show program’s version number and exit