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Download BAM files from TCGA/GDC Legacy Archive using a script
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17 months ago
hsbinf • 20

Hi guys, I need to download a lot of BAM files(~200 cases) from GDC Legacy Archive that were created using Hg19. I've been doing this manually for a few cases to get the feel of the database but I'm trying to figure out if there's a script to do that? I did see the Bioconductor package Genomic Data Commons and TCGAUtils. I think I'm gonna use those to start with but I don't see a way to set the reference genome build as a filter, is there a way to set that or any other tool that might help me? I do have a list of barcodes I want to download and I know how to write a script to get the UUID for those barcodes.

Edit: I did add cases to my cart to download using gdc-client. I'm just looking for an easier way to create a manifest file rather than going through each barcode manually. TIA

tcga gdc-legacy • 122 views

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