Hallo. I am trying to get the TP53 status of the primary tumor samples for my analysis. I saw in a prior thread (https://www.synapse.org/Synapse:syn17038081/discussion/threadId=10222&replyId=29955) that there was an issue with the SNV mapping. I tried to get the TP53 status of primary tumors (TP samples) from variants_passgeno_20220531.csv file by selecting the TP53 region (chr17:7571,739-7,590,808), but only 22 samples appeared. I assume that the reason for this is the mapping issue explained previously, and also, no deletion/inversion data. Would it make sense to try to get the TP53 status from .vcf files, or do they contain the same information? Is there a way I can get raw data to force map the TP53 mutations myself and get structural mutation data, or some other way I can get the TP53 status?
Thank you in advance.