Getting pileup to fastq with indels ala samtools.pl

najoshi · 01-05-2011, 02:03 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.

lh3 · 01-05-2011, 10:42 AM

You have to do this by yourself. Watch out heterozygous indels when we do that.

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01-05-2011, 02:03 AM	#1
najoshi Junior Member Location: Davis, CA Join Date: Feb 2010 Posts: 3	Getting pileup to fastq with indels ala samtools.pl 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.

01-05-2011, 10:42 AM	#2
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 609	You have to do this by yourself. Watch out heterozygous indels when we do that.