I'm trying to merge 2 vcf.gz files and I'm running into a strange behavior using bcftools merge. All of the positions in my second file are being setting to missing (./.) during the merge. Does anyone have any tips for how I might fix this problem?
Here is my command:
bcftools merge -O v -m file1.vcf.gz file2.vcf.gz > out.vcf
Thanks for your help!