Absolutly All positions in mpileup (previously -aa)

[jlapaijmans]

Dear developers,

I am looking to generate a VCF file in which all positions of the reference are represented - so also those where my input bam has no read coverage. In SAMtools mpileup, the option -aa exists which does what I need, but I understand SAMtools mpileup is depricated and shouldn't be used (?). I also am unable to pipe the output from SAMtools mpileup into BCFtools call for generating a VCF, have so far been unable to find another way to convert SAMtools' pileup format to a VCF. Is there a native option in BCFtools mpileup that would result the -aa behaviour from SAMtools, ie resulting in a VCF where all bases of the reference are present?

Any suggestions would be much appreciated! I'm attaching a small example file, in case that helps. XMEN.zip

way to reproduce: bcftools mpileup XMEN1_10.bam -f XMEN-reference_10.fasta

outputs only sites with coverage

samtools mpileup -aa XMEN1_10.bam

outputs all sites (in pileup format I think?)

Many thanks!