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Targeted Calling

By default, octopus will call all contigs specified in the reference index. However, calling can be restricted to a subset of regions by providing a list of regions to call or skip. Note all input regions are assumed to be zero-indexed. If you're using one-indexed regions then add the --one-based-indexing option (applied to all input regions).

--regions (-T) and --skip-regions (-K)#

Provide a list of regions directly to the command line to call or not call. The format is <chr>[:start][-[end]]. So the following are valid:

  • chr1: all of chr1.
  • chr2:10,000,000: the single position 10000000 in chr2.
  • chr3:5,000,000-: everything from chr3:5,000,000 onwards.
  • chr4:100,000,000-200,000,000: everything between chr4:100,000,000 and chr4:200,000,000. The interval is half open so position chr4:200,000,000 is not included.

You can provide multiple regions with this option, for example:

$ octopus -R hs37d5.fa -I NA12878.bam \
-T 1 2:30,000,000- 3:10,000,000-20,000,000

Conversely the --skip-regions is for providing a list of regions not to call. The format is exactly the same as for --regions, so:

$ octopus -R hs37d5.fa -I NA12878.bam -K Y

Will call all contigs in the reference index other than Y. You can provide both --regions and --skip-regions together, in which case the complement of --region and --skip-regions will be used.

tip

The --region option accepts a special ranged argument in the form <lhs> to <rhs> where lhs and rhs are contig names or positions. The reference index is used to expand the range. For example chr1 to chr3 is expanded to chr1 chr2 chr3. You can also specify positional start or end points, e.g., 1:10,000,000 to X. Only one region range can be specified. If it so happens that one of your reference contigs is called to then you cannot use this feature!

--regions-file (-t) and --skip-regions-file (-k)#

These commands accept a file containing a line separated list of regions to call or skip. The regions can either be in the same format as --regions, or in BED format.

$ octopus -R hs37d5.fa -I NA12878.bam -t autosomes.txt
$ octopus -R hs37d5.fa -I NA12878.bam -k avoid.bed
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