I have called SNPs for my samples in tumour samples at time1 and tumour samples at time2 (targeted sequencing) , and I would like to check if there is any significant variations of SNPs in my panel of genes between the two types of samples (many biological replicates per sample). How can I do this? Should I build a matrix of columns (samples) and rows (genes) for SNPs instead of counts like in RNASeq analysis? But how could I notate every mutation found in a gene in order to compare? What kind of analysis is used for this comparison of mutations?
I am completely lost as I have never done something like this, I have just worked with expression. Thanks for your help.
EDIT: I have something like this for each sample:
Chromosome Position Reference Allele Variant Allele Variant Type Sequence Context Consequence dbSNP ID chr1 27022992 A G SNV Interge nic,Coding u pstream_gene_variant,missense_variant chr1 27099846 G GTGCT GTCTCTAT ACACATC Insertion C oding frameshift_variant chr1 27101220 G A SNV Coding missense_variant COSM6604517 ARID1A