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@Sheila , thank you very much for your help! i hope i can manage it now :)
@Sheila thank you very much! I will go with your first suggestion, it seems reasonable and less "painful":) the command is provided and what surprised me that each sample were run only for one chromosome (or maybe i am mistalimg). this is …
the WT sites are not in the vcf files at all, right? then i cannot use them. or am i mistaking smth again?:)
Hi @Sheila , the thing is that im working with the ready vcf files from GDC NIH portal, and i did already quite some job. so, running the new snp analysis will be completely different project:) seems like there is no solution, yet...
Hi @Sheila , thank you again. But I chose the specific set of the sites, so, I need to calculate number of WT cases individually. I guess i will have to dog down t the original bam files. Could you give me na advice: is it, in general, necessarily t…
@Sheila HI, thank you for your answer! now i understand better:) but the problems stays: we downloaded the vcf files after mutect2 analysis from gdc-portal, they were generated using tumor-normal pair. we chose those sites that are interesting to u…