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non-human reference genomes #4

Closed ChristopherRichie closed 10 months ago

ChristopherRichie commented 11 months ago

Ask away!

Can this wf be used with other species reference genomes? (mouse, rat, etc)?

the "FRONT PAGE" says :

The workflow relies on three primary input files:

A reference genome in fasta format An aligned BAM file for the tumor sample An aligned BAM file for the normal sample The reference genome should be either hg19 (GRCh37) or hg38 (GRCh38).

Why are hg19/hg38 suggested here? (is it species-related or formatting-related, etc?)

thanks

RenzoTale88 commented 11 months ago

Hi @ChristopherRichie currently the workflow is designed to work only with these two genome build (hg19 and hg38). We are working on making the component that do not rely on the genome information accessible regardless of the input genome.

ChristopherRichie commented 11 months ago

Thanks.

I am definitely interested in this wf being "species agnostic".

From: Andrea Talenti @.> Sent: Friday, July 28, 2023 10:50 AM To: epi2me-labs/wf-somatic-variation @.> Cc: Richie, Christopher (NIH/NIDA) [E] @.>; Mention @.> Subject: [EXTERNAL] Re: [epi2me-labs/wf-somatic-variation] non-human reference genomes (Issue #4)

Hi @ChristopherRichiehttps://github.com/ChristopherRichie currently the workflow is designed to work only with these two genome build (hg19 and hg38). We are working on making the component that do not rely on the genome information accessible regardless of the input genome.

- Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-somatic-variation/issues/4#issuecomment-1655820545, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AR4COQY7H4TOROECIOTZGVDXSPGTBANCNFSM6AAAAAA22VIJDI. You are receiving this because you were mentioned.Message ID: @.**@.>> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

RenzoTale88 commented 10 months ago

@ChristopherRichie workflow v0.4.0 should be able to run on any species, provided you set --annotation false --classify_insert false. Please let me know if you come across any issue with it. Andrea

ChristopherRichie commented 10 months ago

THANKS. i will give it a try.