Hi. I'm trying to merge .vcf files from TCGA. Each of these files is from a single sample, which is indicated by the file name. However, the vcf file header contains the following for each sample:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
When I try to merge, I get the error:
Error: Duplicate sample names (NORMAL), use --force-samples to proceed anyway.
I could replace NORMAL with the file name so that I can associate each annotation with the correct ID, but I'm wondering if I have to do this. Will --force-samples remove information?