location of required input files

[rod1Gene]

Would you help me find the locations of the required input files for reference 38: hotspots, panel bed, high_confidence_bed, and ensembl_data_dir?

And also the exact 38 reference to which these files refer?

[charlesshale]

All our resources are available here:

https://console.cloud.google.com/storage/browser/hmf-public/HMFtools-Resources/dna_pipeline/

The latest resources files are: https://console.cloud.google.com/storage/browser/_details/hmf-public/HMFtools-Resources/dna_pipeline/v5_32/38/hmf_dna_pipeline_resources.38_v5.32.gz

Each tool gives the list of which specific files are required.

The ref genome is here: https://console.cloud.google.com/storage/browser/_details/hmf-public/HMFtools-Resources/ref_genome/38/

[charlesshale]

That's correct yes. The demo scripts in:

https://github.com/hartwigmedical/hmftools/tree/master/pipeline/scripts

show the arguments/flies passed to each tool for each ref genome version.

Thanks

From: Dave Roe @.> Reply to: hartwigmedical/hmftools @.> Date: Wednesday, 10 May 2023 at 12:20 pm To: hartwigmedical/hmftools @.> Cc: charlesshale @.>, State change @.***> Subject: Re: [hartwigmedical/hmftools] location of required input files (Issue #398)

For SAGE's high_confidence_bed parameter, is it .../variants/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed.gz?

— Reply to this email directly, view it on GitHubhttps://github.com/hartwigmedical/hmftools/issues/398#issuecomment-1541195343, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACSYZZ6II77KWP5U6GTN5KDXFL3PBANCNFSM6AAAAAAX3ZVWZI. You are receiving this because you modified the open/close state.Message ID: @.***>