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.
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.
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