Getting pileup to fastq with indels ala samtools.pl

[najoshi]

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]

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