Entering edit mode
12 days ago
Javier
•
0
Hi, I need to perform HLA typing on the patients from the cohorts of the ICGC ARGO repository, and for that, I require their DNA sequencing reads. I believe I can obtain these reads from their CRAM files of the normal samples, so I downloaded a slice of the CRAM according to their instructions
bin/score-client view --object-id 28358cf3-fba0-51a3-8b93-104bd5d48b23 --reference-file /home/victor/ref-fasta/GRCh38_full_analysis_set_plus_decoy_hla.fa --output-dir /media/victor/c1d5c312-b546-4d5e-b24f-72dbe9e6f18f/javier_CPTAC/per_patien/test
However, it only gives me the header and as a SAM file. Has anyone used the query option and obtained the correct results?
