I was looking into the samtools and bcftools variant callers. When I ran this
samtools mpileup -C 50 -E -t SP DP -u -I -f <ref.genome> -b <bam_list> > <output.bcf>
It told me that flags t, u and I were deprecated. So I thought that bcftools wast the new way to use the "mpileup" but I'm not sure if they are the same.
bcftools mpileup --threads 16 -C 50 -E -f <ref.genome> -b <bam_list> > <output.bcf>
In addition, I realized that the multithreaded flag in the bcftools if only to compress the file. The variant caller will still be single core.
But my question here is what are the differences between
samtools mpileup and