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papaemmelab / toil_cnacs

toil wrapper for CNACS
MIT License
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GRCh38 #1

Open NEOGrok opened 4 years ago

NEOGrok commented 4 years ago

Hi,

We some GRCh38 aligned samples and were wondering if there are any options to make it work with that?

Regards, Francisc

mflevine commented 4 years ago

Hi Francics,

The reference files are all in GRCh37/hg19. I believe if these are converted over to GRCh38 the tool should work as expected. The reference files can be found in the docker container here https://github.com/papaemmelab/docker-cnacs in db.tar.gz. I hope this helps.

Best, Max

NEOGrok commented 4 years ago

Ok, thanks :)

NEOGrok commented 4 years ago

Hi, I've had a look in the db folder, and I'm trying to liftover the files to GRCh38. It's straightforward with the BED files, but I'm not sure what the other files refer to. Is there a description somewhere of what they mean?

Regards, Francisc

RSaikiRSaiki commented 4 years ago

Hi Francics, Hi Max,

I’m Ryunosuke in Kyoto University.

Following information is critical for CNACS. Some files contain genomic coordinates. So they should be translated into GRCh38.

List of SNPs (all.bed) Cytoband information (cytoBand directory) psudoautosomal regions (psudo_auto directory) replication timing (repli_timing directory )

To my knowledge, you don’t have to liftOver other contents.

京都大学 腫瘍生物学 (病理学第二講座) 佐伯龍之介 Department of Pathology and Tumor Biology, Kyoto University Ryunosuke Saiki saikiryunosuke@gmail.com saiki.ryunosuke.57n@st.kyoto-u.ac.jp TEL: 090-4336-2812

2020/06/05 11:27、NEOGrok notifications@github.comのメール:

Hi, I've had a look in the db folder, and I'm trying to liftover the files to GRCh38. It's straightforward with the BED files, but I'm not sure what the other files refer to. Is there a description somewhere of what they mean?

Regards, Francisc

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