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I would like to download top markers for each subpopulation data. Is there no way? It seems different from the DGE data.
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Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf
Check section 1.4.
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Step 1: Go to TCGA in the GDC and open the Cohort Builder
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SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
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UCSC maintains a list of exome probe sets and targets. You could check there:
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Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
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