Investigate: The merge option is currently not set but could cause unexpected behaviour

[berntpopp]

-m, --merge snps|indels|both|snp-ins-del|all|none|id[,]
The option controls what types of multiallelic records can be created. If single asterisk * is appended, the unobserved allele <> or <NON_REF> will be removed at variant sites; if two asterisks ** are appended, the unobserved allele will be removed all sites.

-m none .. no new multiallelics, output multiple records instead

https://samtools.github.io/bcftools/bcftools.html#merge:~:text=%2Dm%2C%20%2D%2Dmerge%20snps%7Cindels%7Cboth%7Csnp%2Dins%2Ddel%7Call%7Cnone%7Cid%5B%2C*%5D