I have two VCF files, each containing somatic mutation calls on each chromosome (ie. the VCFs are not separated by chromosome number or mutation position - they each contain calls on every chromosome) . I want to combine these two files into one. What is the best tool to do this? I tried
bedtools concat but I get this message:
Different number of samples in /path/to/vcf. Perhaps "bcftools merge" is what you are looking for? [W::bcf_hdr_merge] Trying to combine "AD" tag definitions of different lengths
Should I be using the merge function?