I was looking for the same thing, however the -s also gave me the individual bases. I settled with a perl one-liner:
For more complicated things I am using the Bio:: DB::Sam pileup methods.
Hope this helps.
Code:
samtools pileup -cf genome.fasta file.bam |perl -lane 'print join"\t",@F[0..7]'
Hope this helps.
Originally posted by ohofmann
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