I have about 150 bacterial whole genome sequences that I would like to use to create a multi-sample VCF for downstream analysis. I am using BWA to map to the reference genome and then use Pilon to do the variant calling to produce individual VCF files. I am then merging the individual files using bcf tools merge to create a multi-sample VCF. The problem is that positions there are a large number of no calls in the multi-sample vcf because not every strain has a call at every position.
Any suggestions for a better way to create the multi-sample VCF? Thanks in advance!