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

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trombitomi opened this issue Jun 13, 2024 · 1 comment
Open

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

trombitomi opened this issue Jun 13, 2024 · 1 comment
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@trombitomi
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trombitomi commented Jun 13, 2024

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.

@trombitomi
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Dear authors,
Could you provide a template or script to create the reference_panel_cov.fst file?

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