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?
Thanks,
Michael Gormley
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?
Thanks,
Michael Gormley
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