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