I am confused about how to perform a functional analysis after a variant calling on a cohort of patients. I have anotated all vcfs and filter them in order to get only those deleterious variants.
I was thinking on merging those vcf:
I tried to merge them with
bcftools merge and also using
VariantAnnotation and transforming each sample vcf into a dataframe containing the variant lines to then row bind all those dataframes together.
As an example, Ill show some fields of teh first row of a dataframe:
CHROM START REF ALT FILTER DP GENEID SIFT 17 1000 T A PASS 62 TP53 0
Then, I would extract the genes affected by those variants and perform a gene set enrichment analysis, a pathway analysis similar to those performed after an RNA-seq analysis (with
enrichR, for example). But I am confused about the viability of this steps. For example, I would like that, during the pathways analysis, the program I use not just reads the list of mutated genes in my cohort, but also takes into account that, if a gene is mutated in more than one sample, it should wheight more in the analysis than a gene which appears in just one sample.