I am trying to get base coverage information, and am using the
--PER_BASE_COVERAGE output from Picard tools to get a text file of base level coverage. However, some of my targets are being grouped together. In the targets file, these are separated by one base as such:
12 12258595 12258695 + TARGET1 12 12258696 12258795 + TARGET2 12 12258796 12259791 + TARGET3
However, when I look at my covg file, I see the following:
chr pos target covg 12 12258595 TARGET1|TARGET2|TARGET3 510
Why would HSmetrics group these targets together, and how can I separate them?