Are there any alignment programs that take SNPs into account during alignment?

[sdarko]

I was recently looking through some mRNA-Seq alignments in IGV that I made with TopHat and I loaded up the SNP track to compare some alignment mismatches to known SNPs. I was looking at it and it occurred to me that, to an alignment algorithm aligning against a reference genome, SNPs and mismatches would look the same so that a read that had a real SNP and a base call error would look like a read with two mismatches and (possibly) wouldn't align.

So, are there any alignment programs that take SNPs into account during alignment by, say, using SNP tracks as an optional input?

[Simon Anders]

How about GSNAP? You can pass it a list of SNPs in addition to the reference.

Thomas D. Wu and Serban Nacu
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Bioinformatics 2010 26: 873-881

[lh3]

gsnap, mosaik and novoalign