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CCRGeneticsBranch / Oncogenomics_v2

Oncogenomics portal version 2
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HG38 support #6

Open hsienchao opened 1 year ago

hsienchao commented 1 year ago

Manually upload two cases

  1. NCI0263/Tumor5 https://fsabcl-onc01d.ncifcrf.gov/clinomicsd/public/viewPatient/22112/NCI0263/any
  2. CL0082/OM16-043 https://fsabcl-onc01d.ncifcrf.gov/clinomicsd/public/viewPatient/null/CL0082

Items finished:

  1. Updated uploadCase.pl script. Added "genome_version" column in case table.
  2. Updated viewCase page. Added "genome version" label
  3. Created hg38_annot_oc table. Imported hg38 OC annotation data.
  4. Updated var_sample_avia_oc table. Now it can take both hg19 and hg38 annotation data.
  5. Added hg38 gene data to gene table. The version is gencode v38.
  6. Updated cnv_genes and cnvkit_genes table. Now it joins both hg19 and hg38 gene data.
  7. Updated refreshView.pl

To do:

  1. Figure out why there are so many unannotated variants in these two cases.
  2. Modify IGV views to support hg38. (Need bam files which were deleted previously. Vineela will recreate them)
  3. Update domain information (if necessary)
  4. Project level TMM scripts need to be changed. (Or keep TPM only)
hsienchao commented 1 year ago

The hg38 missing variant list is attached.

hg38_not_found_variants.txt