search

VanLoo-lab / CAMDAC

GNU General Public License v3.0
11 stars 5 forks source link

How to create reference panel coverage file (.fst)? #14

Open trombitomi opened 3 weeks ago

trombitomi commented 3 weeks ago

Dear Authors,

In your manual you refer to reference_panel_cov:

# For hg19 aligned reads, you may use the example file at:
# file.path(path_to_CAMDAC,"pipeline_files","example_data", 
# paste0("normal_lung_cov_",sex,".fst"))

Instead of this, I have found another .fst file: CAMDAC/pipeline_files/msp1_fragments/msp1_fragments_RRBS_hg38.fst in your repo. I would like to create my own coverage reference from our data, can you provide code / method to do this?

Thanks in advance! Best, Tamas

EDIT: I have realised the msp1_fragments file has a different file structure, whereas the reference_panel_cov is more similar to a .vcf (?). Still curious how to create the reference panel .fst file.