Getting pileup to fastq with indels ala samtools.pl

najoshi

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Join Date: Feb 2010

Posts: 20
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#1

Getting pileup to fastq with indels ala samtools.pl

01-05-2011, 03:03 AM

Hi all,

So I need a program that will essentially do the functionality of samtools.pl pileup2fq, but I need it to take into account indels. It appears that pileup2fq only uses indels to determine whether or not to upcase or lowcase the output flanking sequence bases. What I need is a program that will actually take into account the indels and create an output fastq/a file that will have the insertions inserted and the deletions deleted. Is there such a program out there somewhere? As far as I can tell samtools.pl does not do this.

- Nik.
Tags: indels, pileup, samtools
lh3

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Join Date: Feb 2008

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01-05-2011, 11:42 AM

You have to do this by yourself. Watch out heterozygous indels when we do that.
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Getting pileup to fastq with indels ala samtools.pl

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