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Old 02-01-2012, 07:58 AM   #1
Location: Seoul

Join Date: Jan 2012
Posts: 42
Post what's difference between 'pileup' and 'mpileup' at samtools?

Does anyone know what's different?

'pileup' command shows output '*.bcf'

'mpileup' command shows output '*.bci'

as i understand, mpileup is multi-input version of pileup. however, the output file shows different format.
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Old 02-01-2012, 08:24 AM   #2
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pileup was deprecated in v.1.17. It is now mpileup. You can still run mpileup on a single bam though.
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Old 02-01-2012, 08:24 AM   #3
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pileup is deprecated. Don't use it. Use mpileup.
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