check bcftools consensus generation / ambiguity calls

[MarieLataretu]

Current parameter: bcftools consensus [...] --sample {name} -I VCF with FORMAT/GT and exactly one sample

Differences -I/-H I:

• -I applies REF+ALT regardless of the genotype
• -H I uses FORMAT/GT

(https://github.com/samtools/bcftools/issues/1708#issuecomment-1114804855, https://github.com/samtools/bcftools/issues/1400#issuecomment-777286784)

Should we use --sample {name} -H I instead of --sample {name} -I, because FORMAT/GT is not considered?

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Related issues: https://github.com/samtools/bcftools/issues/1516 https://github.com/samtools/bcftools/issues/1400 https://github.com/samtools/bcftools/issues/1708

Manual: http://samtools.github.io/bcftools/bcftools.html#consensus

[MarieLataretu]

Test results:

no FORMAT/GT, no --sample	FORMAT/GT, no --sample	FORMAT/GT, --sample
-I	IUPAC REF + all ALT	IUPAC REF + all ALT	IPUAC GT *)
-H I	REF	na	IPUAC GT *)

*) of respective sample

-> -I/-H I makes no difference, if there is also --sample {name}

I'd rather switch to -H I though, because it's more explicit for what we want