Hi Takafumi NAKANE,
Thanks for reaching out!
We have this in most of the mutation data files:
・Number of reads matching the reference allele.
・Number of reads matching the alternate allele.
See e.g.:
The columns are:
- t_ref_count, t_alt_count, n_ref_count, n_alt_count
See also:
https://docs.cbioportal.org/file-formats/#mutation-data
We don’t have this easily accessible:
・Major copy number of segment overlapping mutation.
・Minor copy number of segment overlapping mutation.
・Total copy number of segment in healthy tissue.
We do have segmented copy number data. E.g.:
https://github.com/cBioPortal/datahub/blob/master/public/ov_tcga/data_cna_hg19.seg
and documentation:
https://docs.cbioportal.org/file-formats/#segmented-data
But this is prolly not exactly what you want. We are working on incorporating the type of information you requested into cBioPortal, but there are no public studies available yet
Thanks!
Ino
URL:
https://www.dna-chip.co.jp/en/
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