I'm running a pipeline that uses a very old version of samtools mpileup version 1.6. When we switched to the more modern bcftools mpileup version 1.16 we noticed that the data changed slightly, for example some of the lower frequency calls that used to have 2 supporting reads now only have 1 or vice versa. Although the shifts in data are very subtle, we would like to set the bcftools mpileup commands so that it produces an outputs exactly like the old samtools mpileup. I don't expect anyone here to know what these exact parameters are, but I was wondering if anyone had any general guidance on how the mpileup command differs between samtools and bcftools. Searching the readme.txt files between releases it seems that mpileup had a number of updates on how indels were detected and I see some of the defaults changed (i.e. min-iread default is 2 instead of 1, gap-frac is 0.05 instead of 0.002, etc. etc.) However, even when I explicitly set the values for the arguments in which the defaults changed, I can never exactly mimic the old output. Would it even be possible to do this? Any advice would be appreciated. Thanks!
Nate
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