Hi,
I'm trying to parse the Samtools Pileup format in Perl.
I've created a paired-end assembly using BWA (aln, sampe) and then used Samtools to create a pileup (using import - sort - index - pileup).
What I want to do is to open up the pileup (which is obviously in the Samtools Pileup format) and iterate over each position of the pileup, examining differences in base-calls.
Does anyone know of anything available, or have and sample code they could post?
Many thanks.
I'm trying to parse the Samtools Pileup format in Perl.
I've created a paired-end assembly using BWA (aln, sampe) and then used Samtools to create a pileup (using import - sort - index - pileup).
What I want to do is to open up the pileup (which is obviously in the Samtools Pileup format) and iterate over each position of the pileup, examining differences in base-calls.
Does anyone know of anything available, or have and sample code they could post?
Many thanks.
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