Hello all, I am trying to find DNA-seq bam file and RNA-seq bam file from one sample. I also need vcf file for SNV callset. I am looking for some examples from TCGA data. It would be great if anyone could point out a paper that use dataset of this kind. Thanks for your help, --Subhajit
3 answers
Genomic data commons: https://gdc.cancer.gov/
But you won't be able to get the bam or germline variant calls unless you have dbGap approval. Regardless all the other level 3 data is available for public download. Also bioconductor has a good package called TCGAbiolinks.
Thanks for your answer. We do have controlled data access. I am using GDC with the token to get level 1/2 data.
I wanna know, if anyone knows about a good data set (a set of samples) with both DNA-seq and RNA-seq bam files and vcf file with snv call.
Thank you !! I will try that and let you know. Thanks for your helpful comment !
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