How to download all the VCFs generated from WXS BAM in TCGA legacy archive?
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4.2 years ago
Jackie ▴ 70

How to download all the VCFs associated with the WXS BAM files? In the legacy archive in GDC portal, if you select 'WXS' under 'Experimental Strategy', only BAM files are kept (e.g., no VCFs ). Usually, there are two BAM files labelled as 'WXS', one should be the tumor sample, the other should be the matched-normal sample. However, what is the right way to find out which VCFs are associated with these WXS BAM files? usually, there are multiple VCFs for each case, and seems there is no straightforward way to apply any filters in the GDC portal to get only the VCFs associated with these two WXS BAM files. Can anyone suggest how to do it?


TCGA WXS VCFs • 1.2k views

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