Converting ICGC ids to TCGA format

Question

[hadas.samuels]

Hello,

I'm working with vcf files of WGS of cancer cells, their names are in TCGA format. I recently started working with RNA expression files, and their names are in ICGC format. How can I transform from this 2 formats?

Thanks in advance

[GenoMax]

Please provide examples when referring to ID of any kind.

[hadas.samuels]

OK. I'm adding here a row from an excel I have for the conversions (i'm missing there many TCGA ids, thats why I need the help...):

donor_unique_id                                donor_wgs_exclusion_white_gray  submitter_donor_id                    icgc_donor_id  dcc_project_code  aliquot_id                            submitter_specimen_id                 icgc_specimen_id  submitter_sample_id                   icgc_sample_id  dcc_specimen_type              library_strategy  short_id       TCGA_filename
BLCA-US::178b28cd-99c3-48dc-8d09-1ef71b4cee80  Whitelist                       178b28cd-99c3-48dc-8d09-1ef71b4cee80  DO555          BLCA-US           4838b5a9-968c-4178-bffb-3fafe1f6dc09  59d6683f-5eb7-493d-8e8e-78b88be2cd70  SP1132            4838b5a9-968c-4178-bffb-3fafe1f6dc09  SA1556          Primary tumour - solid tissue  WGS               4838b5a9-968c  f053fb4b-192f-5c2e-aff6-e0c7d6443faf
BLCA-US::1e308b12-0590-4dae-94d0-a539fcf25df7  Whitelist                       1e308b12-0590-4dae-94d0-a539fcf25df7  DO479          BLCA-US           c66c92d5-df65-46e6-861d-d8a98808e6a3  e9889071-4c6e-4761-9d65-06c6b5989fb7  SP967             c66c92d5-df65-46e6-861d-d8a98808e6a3  SA3742          Primary tumour - solid tissue  WGS               c66c92d5-df65  c84b676a-a409-517f-9920-b63119f1f717
BLCA-US::24f21425-b001-4986-aedf-5b4dd851c6ad  Whitelist                       24f21425-b001-4986-aedf-5b4dd851c6ad  DO689          BLCA-US           973d0577-8ca4-44a1-817f-1d3c1bada151  967443e3-35c3-4f41-9bb5-dc899d290806  SP1419            973d0577-8ca4-44a1-817f-1d3c1bada151  SA3721          Primary tumour - solid tissue  WGS               973d0577-8ca4  0f84d32c-171e-5837-ada0-55d4a3e8d3a1

I'm looking at columns 4/10 for the ICGC id, and the last column for the TCGA id.

Thanks in advance

Answer 1

[Zhenyu Zhang]

The aliquot_ids and submitter_ids seem to be cghub ids