Hi all,
I’m exploring multiple ways of calculating allele/site frequency spectra from
exome capture data. The most recent details describing this in SAMtools comes
from the multisample SNP calling page from 2010:
http://samtools.sourceforge.net/mpileup.shtml
<http://samtools.sourceforge.net/mpileup.shtml>
I’ve found papers as late as December 2013 using SAMtools/BCFtools v0.1.16
using this approach. Things have obviously changed in 1.0+, most notably
several calls and the ability to specify a prior. Is it still possible to
perform an iterative Bayesian estimation of the AFS in the current version of
SAMtools? Is v1.0+ even used for this type of analysis anymore?
Any clarification would be appreciated!
Thanks,
Brice
---------------
Brice A. J. Sarver, Ph.D.
Postdoctoral Research Associate - Good Lab
University of Montana
Division of Biological Sciences
32 Campus Drive, Health Sciences 104
Missoula, MT, 59812
Office: Health Sciences 308
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