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Old 02-27-2012, 02:56 PM   #1
Location: Philadelphia

Join Date: Feb 2012
Posts: 19
Default samtools pileup manual description

Hello all,

I am trying to use a shell script that calls samtools pileup function. Because the pileup function is deprecated, the shell script produces nonsense output. I would like to translate the line that calls pileup into a line calling mpileup that produces the same output. Unfortunately, I can not find any detailed information on the pileup command line arguments. The offending line is listed below:

samtools pileup -c -f $FA -r 0.0000007 -l $BED $BAM > $PILEUP

in which $FA is the reference fasta file, $BED is a file formatted for the l option of pileup, $BAM is the bam file and $pileup is the pileup file to write to.

Does anyone know what the -c and -r arguments refer to under the deprecated pileup function and if this call can be converted into a call to mpileup and produce the same output?

Michael Gormley
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Old 02-27-2012, 05:48 PM   #2
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Location: Sydney

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Posts: 149


I was troubleshooting this on another issue. Installing version 0.1.16 samtools gave me:

Usage: samtools pileup [options] <in.bam>|<in.sam>

Option: -s simple (yet incomplete) pileup format
-S the input is in SAM
-B disable BAQ computation
-A use the original MAQ model for SNP calling (DEPRECATED)
-2 output the 2nd best call and quality
-i only show lines/consensus with indels
-Q INT min base quality (possibly capped by BAQ) [13]
-C INT coefficient for adjusting mapQ of poor mappings [0]
-m INT filtering reads with bits in INT [0x704]
-M INT cap mapping quality at INT [60]
-d INT limit maximum depth for indels [1024]
-t FILE list of reference sequences (force -S)
-l FILE list of sites at which pileup is output
-f FILE reference sequence in the FASTA format

-c compute the consensus sequence
-v print variants only (for -c)
-g output in the GLFv3 format (DEPRECATED)
-T FLOAT theta in maq consensus calling model (for -c) [0.83]
-N INT number of haplotypes in the sample (for -c) [2]
-r FLOAT prior of a difference between two haplotypes (for -c) [0.001]
-G FLOAT prior of an indel between two haplotypes (for -c) [0.00015]
-I INT phred prob. of an indel in sequencing/prep. (for -c) [40]

hope that helps.
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Old 04-25-2013, 08:33 PM   #3
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Location: Seoul, Korea

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Posts: 1

I am on the same boat. I am trying to revise the shell script that uses depreciated pileup function you mentioned. Did you by any chance figure out how to replace it with mpileup command? Any help would be appreciated. Thanks.
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manual, pileup, samtools

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