clarify data source for HSat annotation

human-pangenomics / hpp_production_workflows

WDL’s and Dockerfiles for assembly QC process

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clarify data source for HSat annotation #7

Closed ptrebert closed 6 months ago

ptrebert commented 2 years ago

Hi, could you please clarify the data source for the chm13v1.1/HSat annotation used in this step:

2. Incorporating HSATs Coverage Bias
[...]
To do so we need a bed file pointing to the HSat in the reference then we can run the script project_blocks.py to project it back to the assembly.

Or is that already packaged in the container? Thanks! +Peter

mobinasri commented 1 year ago

@ptrebert Sorry for the delay. I missed this issue. You can find the bed files pointing to the HSat coverage-biased blocks here: https://github.com/mobinasri/flagger/tree/main/misc/biased_regions They are in the CHM13-v1.1 coordinates.