How to force bcftools to call all variants

1

Hello
I am using bcftools to call variants with this command:

bcftools mpileup   -Ou -b bamlist  -f ref.fasta  | bcftools call -Ob    -mv   >variant.bcf

However, for some specific variants that I know to exist (looking at bam files with IGV), I do not get variant calls. The read depth is shallow 3-4 reads per site. How do I force bcftools to output all possible variants, even tough they have low probability?


calling


bcftools


mpileup


variant


call

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