I have been assigned whole genome sequencing data of tumour samples of responder and non-responder patients to a drug exactly with this data file;
case_rna_ids.txt pheno.copynumber.caveman.csv.tar pheno.passed.somatic.indel.vcf.tar pheno.snv.pass.vcf.tar pheno.SVannotated.txt.tar pheno_case_dna_rna_ids.txt pheno_case_rna_ids.txt pheno_dna_mut_sigs.txt pheno_rna_rpkm.txt.tar rna_rpkm.txt copy.tar rna_rpkm.txt.tar trg.passed.somatic.indels.vcf.tar trg.snp.pass.vcf.tar trg_case_dna_ids.txt
I am googling, I guess I should annotate these mutations to see which one affects the gene expression. I uploaded one of
Ensembl Variant Effect Predictor (VEP) and job is running likely finishing one ticket takes long time though.
Anyone please have experience with such files to tell me how could I start?